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Domain of microorganisms
This article is about the microorganisms. For the genus, see Bacterium (genus). For other uses, see Bacteria (disambiguation).

Bacteria
Temporal range: Archean–Present
3500–0 Ma
Pha.
Proterozoic
Archean
Had.
[1]
Scanning electron micrograph of Escherichia coli rods
Scientific classification Edit this classification
Domain: Bacteria
Woese et al. 1990
Phyla

See § Phyla

Synonyms
  • "Bacteria" (Cohn 1872) Cavalier-Smith 1983
  • "Bacteria" Haeckel 1894
  • "Bacteria" Cavalier-Smith 2002
  • "Bacteriaceae" Cohn 1872a
  • "Bacteriobionta" Möhn 1984
  • "Bacteriophyta" Schussnig 1925
  • "Eubacteria" Woese and Fox 1977
  • "Neobacteria" Möhn 1984
  • "Schizomycetaceae" de Toni and Trevisan 1889
  • "Schizomycetes" Nägeli 1857

Bacteria (/bækˈtɪəriə/ ⓘ; SG: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria play a vital role in many stages of the nutrient cycle by recycling nutrients and the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised and there are many species that cannot be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.

Humans and most other animals carry vast numbers (approximately 1013 to 1014) of bacteria.[2] Most are in the gut, and there are many on the skin. Most of the bacteria in and on the body are harmless or rendered so by the protective effects of the immune system, and many are beneficial,[3] particularly the ones in the gut. However, several species of bacteria are pathogenic and cause infectious diseases, including cholera, syphilis, anthrax, leprosy, tuberculosis, tetanus and bubonic plague. The most common fatal bacterial diseases are respiratory infections. Antibiotics are used to treat bacterial infections and are also used in farming, making antibiotic resistance a growing problem. Bacteria are important in sewage treatment and the breakdown of oil spills, the production of cheese and yogurt through fermentation, the recovery of gold, palladium, copper and other metals in the mining sector, as well as in biotechnology, and the manufacture of antibiotics and other chemicals.

Once regarded as plants constituting the class Schizomycetes ("fission fungi"), bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and rarely harbour membrane-bound organelles. Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotes consist of two very different groups of organisms that evolved from an ancient common ancestor. These evolutionary domains are called Bacteria and Archaea.[4]

Etymology

Rod-shaped Bacillus subtilis

The word bacteria is the plural of the Neo-Latin bacterium, which is the Latinisation of the Ancient Greek βακτήριον (baktḗrion),[5] the diminutive of βακτηρία (baktēría), meaning "staff, cane",[6] because the first ones to be discovered were rod-shaped.[7][8]

Origin and early evolution

Main article: Evolution of bacteria
Further information: Earliest known life forms, Evolutionary history of life, and Timeline of evolution
Phylogenetic tree of Bacteria, Archaea and Eucarya, with the last universal common ancestor at the root.[9]

The ancestors of bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, about 4 billion years ago.[10] For about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life.[11][12][13] Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the history of bacterial evolution, or to date the time of origin of a particular bacterial species. However, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage.[14] The most recent common ancestor of bacteria and archaea was probably a hyperthermophile that lived about 2.5 billion–3.2 billion years ago.[15][16][17] The earliest life on land may have been bacteria some 3.22 billion years ago.[18]

Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes.[19][20] Here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea.[21][22] This involved the engulfment by proto-eukaryotic cells of alphaproteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still found in all known Eukarya (sometimes in highly reduced form, e.g. in ancient "amitochondrial" protozoa). Later, some eukaryotes that already contained mitochondria also engulfed cyanobacteria-like organisms, leading to the formation of chloroplasts in algae and plants. This is known as primary endosymbiosis.[23]

Habitat

Bacteria are ubiquitous, living in every possible habitat on the planet including soil, underwater, deep in Earth's crust and even such extreme environments as acidic hot springs and radioactive waste.[24][25] There are approximately 2×1030 bacteria on Earth,[26] forming a biomass that is only exceeded by plants.[27] They are abundant in lakes and oceans, in arctic ice, and geothermal springs[28] where they provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy.[29] They live on and in plants and animals. Most do not cause diseases, are beneficial to their environments, and are essential for life.[3][30] The soil is a rich source of bacteria and a few grams contain around a thousand million of them. They are all essential to soil ecology, breaking down toxic waste and recycling nutrients. They are even found in the atmosphere and one cubic metre of air holds around one hundred million bacterial cells. The oceans and seas harbour around 3 x 1026 bacteria which provide up to 50% of the oxygen humans breathe.[31] Only around 2% of bacterial species have been fully studied.[32]

Extremophile bacteria
Habitat Species Reference
Cold (minus 15 °C Antarctica) Cryptoendoliths [33]
Hot (70–100 °C geysers) Thermus aquaticus [32]
Radiation, 5MRad Deinococcus radiodurans [33]
Saline, 47% salt (Dead Sea, Great Salt Lake) several species [32][33]
Acid pH 3 several species [24]
Alkaline pH 12.8 betaproteobacteria [33]
Space (6 years on a NASA satellite) Bacillus subtilis [33]
3.2 km underground several species [33]
High pressure (Mariana Trench – 1200 atm) Moritella, Shewanella and others [33]

Morphology

Further information: Bacterial cell structure § Cell morphology
a diagram showing bacteria morphology
Bacteria display many cell morphologies and arrangements[8]

Size. Bacteria display a wide diversity of shapes and sizes. Bacterial cells are about one-tenth the size of eukaryotic cells and are typically 0.5–5.0 micrometres in length. However, a few species are visible to the unaided eye—for example, Thiomargarita namibiensis is up to half a millimetre long,[34] Epulopiscium fishelsoni reaches 0.7 mm,[35] and Thiomargarita magnifica can reach even 2 cm in length, which is 50 times larger than other known bacteria.[36][37] Among the smallest bacteria are members of the genus Mycoplasma, which measure only 0.3 micrometres, as small as the largest viruses.[38] Some bacteria may be even smaller, but these ultramicrobacteria are not well-studied.[39]

Shape. Most bacterial species are either spherical, called cocci (singular coccus, from Greek kókkos, grain, seed), or rod-shaped, called bacilli (sing. bacillus, from Latin baculus, stick).[40] Some bacteria, called vibrio, are shaped like slightly curved rods or comma-shaped; others can be spiral-shaped, called spirilla, or tightly coiled, called spirochaetes. A small number of other unusual shapes have been described, such as star-shaped bacteria.[41] This wide variety of shapes is determined by the bacterial cell wall and cytoskeleton and is important because it can influence the ability of bacteria to acquire nutrients, attach to surfaces, swim through liquids and escape predators.[42][43]

The range of sizes shown by prokaryotes (Bacteria), relative to those of other organisms and biomolecules.[44]

Multicellularity. Most bacterial species exist as single cells; others associate in characteristic patterns: Neisseria forms diploids (pairs), streptococci form chains, and staphylococci group together in "bunch of grapes" clusters. Bacteria can also group to form larger multicellular structures, such as the elongated filaments of Actinomycetota species, the aggregates of Myxobacteria species, and the complex hyphae of Streptomyces species.[45] These multicellular structures are often only seen in certain conditions. For example, when starved of amino acids, myxobacteria detect surrounding cells in a process known as quorum sensing, migrate towards each other, and aggregate to form fruiting bodies up to 500 micrometres long and containing approximately 100,000 bacterial cells.[46] In these fruiting bodies, the bacteria perform separate tasks; for example, about one in ten cells migrate to the top of a fruiting body and differentiate into a specialised dormant state called a myxospore, which is more resistant to drying and other adverse environmental conditions.[47]

Biofilms. Bacteria often attach to surfaces and form dense aggregations called biofilms,[48] and larger formations known as microbial mats.[49] These biofilms and mats can range from a few micrometres in thickness to up to half a metre in depth, and may contain multiple species of bacteria, protists and archaea. Bacteria living in biofilms display a complex arrangement of cells and extracellular components, forming secondary structures, such as microcolonies, through which there are networks of channels to enable better diffusion of nutrients.[50][51] In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms.[52] Biofilms are also important in medicine, as these structures are often present during chronic bacterial infections or in infections of implanted medical devices, and bacteria protected within biofilms are much harder to kill than individual isolated bacteria.[53]

Cellular structure

Further information: Bacterial cell structure
Prokaryote cell with structure and parts
Structure and contents of a typical Gram-positive bacterial cell (seen by the fact that only one cell membrane is present).

Intracellular structures

The bacterial cell is surrounded by a cell membrane, which is made primarily of phospholipids. This membrane encloses the contents of the cell and acts as a barrier to hold nutrients, proteins and other essential components of the cytoplasm within the cell.[54] Unlike eukaryotic cells, bacteria usually lack large membrane-bound structures in their cytoplasm such as a nucleus, mitochondria, chloroplasts and the other organelles present in eukaryotic cells.[55] However, some bacteria have protein-bound organelles in the cytoplasm which compartmentalize aspects of bacterial metabolism,[56][57] such as the carboxysome.[58] Additionally, bacteria have a multi-component cytoskeleton to control the localisation of proteins and nucleic acids within the cell, and to manage the process of cell division.[59][60][61]

Many important biochemical reactions, such as energy generation, occur due to concentration gradients across membranes, creating a potential difference analogous to a battery. The general lack of internal membranes in bacteria means these reactions, such as electron transport, occur across the cell membrane between the cytoplasm and the outside of the cell or periplasm.[62] However, in many photosynthetic bacteria, the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane.[63] These light-gathering complexes may even form lipid-enclosed structures called chlorosomes in green sulfur bacteria.[64]

An electron micrograph of Halothiobacillus neapolitanus cells with carboxysomes inside, with arrows highlighting visible carboxysomes. Scale bars indicate 100 nm.

Bacteria do not have a membrane-bound nucleus, and their genetic material is typically a single circular bacterial chromosome of DNA located in the cytoplasm in an irregularly shaped body called the nucleoid.[65] The nucleoid contains the chromosome with its associated proteins and RNA. Like all other organisms, bacteria contain ribosomes for the production of proteins, but the structure of the bacterial ribosome is different from that of eukaryotes and archaea.[66]

Some bacteria produce intracellular nutrient storage granules, such as glycogen,[67] polyphosphate,[68] sulfur[69] or polyhydroxyalkanoates.[70] Bacteria such as the photosynthetic cyanobacteria, produce internal gas vacuoles, which they use to regulate their buoyancy, allowing them to move up or down into water layers with different light intensities and nutrient levels.[71]

Extracellular structures

Further information: Cell envelope

Around the outside of the cell membrane is the cell wall. Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by peptides containing D-amino acids.[72] Bacterial cell walls are different from the cell walls of plants and fungi, which are made of cellulose and chitin, respectively.[73] The cell wall of bacteria is also distinct from that of achaea, which do not contain peptidoglycan. The cell wall is essential to the survival of many bacteria, and the antibiotic penicillin (produced by a fungus called Penicillium) is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan.[73]

There are broadly speaking two different types of cell wall in bacteria, that classify bacteria into Gram-positive bacteria and Gram-negative bacteria. The names originate from the reaction of cells to the Gram stain, a long-standing test for the classification of bacterial species.[74]

Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and teichoic acids. In contrast, Gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins. Most bacteria have the Gram-negative cell wall, and only members of the Bacillota group and actinomycetota (previously known as the low G+C and high G+C Gram-positive bacteria, respectively) have the alternative Gram-positive arrangement.[75] These differences in structure can produce differences in antibiotic susceptibility; for instance, vancomycin can kill only Gram-positive bacteria and is ineffective against Gram-negative pathogens, such as Haemophilus influenzae or Pseudomonas aeruginosa.[76] Some bacteria have cell wall structures that are neither classically Gram-positive or Gram-negative. This includes clinically important bacteria such as mycobacteria which have a thick peptidoglycan cell wall like a Gram-positive bacterium, but also a second outer layer of lipids.[77]

In many bacteria, an S-layer of rigidly arrayed protein molecules covers the outside of the cell.[78] This layer provides chemical and physical protection for the cell surface and can act as a macromolecular diffusion barrier. S-layers have diverse functions and are known to act as virulence factors in Campylobacter species and contain surface enzymes in Bacillus stearothermophilus.[79][80]

Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface
Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface

Flagella are rigid protein structures, about 20 nanometres in diameter and up to 20 micrometres in length, that are used for motility. Flagella are driven by the energy released by the transfer of ions down an electrochemical gradient across the cell membrane.[81]

Fimbriae (sometimes called "attachment pili") are fine filaments of protein, usually 2–10 nanometres in diameter and up to several micrometres in length. They are distributed over the surface of the cell, and resemble fine hairs when seen under the electron microscope.[82] Fimbriae are believed to be involved in attachment to solid surfaces or to other cells, and are essential for the virulence of some bacterial pathogens.[83] Pili (sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called conjugation where they are called conjugation pili or sex pili (see bacterial genetics, below).[84] They can also generate movement where they are called type IV pili.[85]

Glycocalyx is produced by many bacteria to surround their cells,[86] and varies in structural complexity: ranging from a disorganised slime layer of extracellular polymeric substances to a highly structured capsule. These structures can protect cells from engulfment by eukaryotic cells such as macrophages (part of the human immune system).[87] They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.[88]

The assembly of these extracellular structures is dependent on bacterial secretion systems. These transfer proteins from the cytoplasm into the periplasm or into the environment around the cell. Many types of secretion systems are known and these structures are often essential for the virulence of pathogens, so are intensively studied.[88]

Endospores

Further information: Endospore
Anthrax stained purple
Bacillus anthracis (stained purple) growing in cerebrospinal fluid[89]

Some genera of Gram-positive bacteria, such as Bacillus, Clostridium, Sporohalobacter, Anaerobacter, and Heliobacterium, can form highly resistant, dormant structures called endospores.[90] Endospores develop within the cytoplasm of the cell; generally, a single endospore develops in each cell.[91] Each endospore contains a core of DNA and ribosomes surrounded by a cortex layer and protected by a multilayer rigid coat composed of peptidoglycan and a variety of proteins.[91]

Endospores show no detectable metabolism and can survive extreme physical and chemical stresses, such as high levels of UV light, gamma radiation, detergents, disinfectants, heat, freezing, pressure, and desiccation.[92] In this dormant state, these organisms may remain viable for millions of years.[93][94][95] Endospores even allow bacteria to survive exposure to the vacuum and radiation of outer space, leading to the possibility that bacteria could be distributed throughout the Universe by space dust, meteoroids, asteroids, comets, planetoids, or directed panspermia.[96][97]

Endospore-forming bacteria can cause disease; for example, anthrax can be contracted by the inhalation of Bacillus anthracis endospores, and contamination of deep puncture wounds with Clostridium tetani endospores causes tetanus, which, like botulism, is caused by a toxin released by the bacteria that grow from the spores.[98] Clostridioides difficile infection, a common problem in healthcare settings, is caused by spore-forming bacteria.[99]

Metabolism

Further information: Microbial metabolism

Bacteria exhibit an extremely wide variety of metabolic types.[100] The distribution of metabolic traits within a group of bacteria has traditionally been used to define their taxonomy, but these traits often do not correspond with modern genetic classifications.[101] Bacterial metabolism is classified into nutritional groups on the basis of three major criteria: the source of energy, the electron donors used, and the source of carbon used for growth.[102]

Phototrophic bacteria derive energy from light using photosynthesis, while chemotrophic bacteria breaking down chemical compounds through oxidation,[103] driving metabolism by transferring electrons from a given electron donor to a terminal electron acceptor in a redox reaction. Chemotrophs are further divided by the types of compounds they use to transfer electrons. Bacteria that derive electrons from inorganic compounds such as hydrogen, carbon monoxide, or ammonia are called lithotrophs, while those that use organic compounds are called organotrophs.[103] Still, more specifically, aerobic organisms use oxygen as the terminal electron acceptor, while anaerobic organisms use other compounds such as nitrate, sulfate, or carbon dioxide.[103]

Many bacteria, called heterotrophs, derive their carbon from other organic carbon. Others, such as cyanobacteria and some purple bacteria, are autotrophic, meaning they obtain cellular carbon by fixing carbon dioxide.[104] In unusual circumstances, the gas methane can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism.[105]

Nutritional types in bacterial metabolism
Nutritional type Source of energy Source of carbon Examples
 Phototrophs  Sunlight  Organic compounds (photoheterotrophs) or carbon fixation (photoautotrophs)  Cyanobacteria, Green sulfur bacteria, Chloroflexota, or Purple bacteria 
 Lithotrophs Inorganic compounds  Organic compounds (lithoheterotrophs) or carbon fixation (lithoautotrophs)  Thermodesulfobacteriota, Hydrogenophilaceae, or Nitrospirota 
 Organotrophs Organic compounds  Organic compounds (chemoheterotrophs) or carbon fixation (chemoautotrophs)    Bacillus, Clostridium, or Enterobacteriaceae 

In many ways, bacterial metabolism provides traits that are useful for ecological stability and for human society. For example, diazotrophs have the ability to fix nitrogen gas using the enzyme nitrogenase.[106] This trait, which can be found in bacteria of most metabolic types listed above,[107] leads to the ecologically important processes of denitrification, sulfate reduction, and acetogenesis, respectively.[108] Bacterial metabolic processes are important drivers in biological responses to pollution; for example, sulfate-reducing bacteria are largely responsible for the production of the highly toxic forms of mercury (methyl- and dimethylmercury) in the environment.[109] Nonrespiratory anaerobes use fermentation to generate energy and reducing power, secreting metabolic by-products (such as ethanol in brewing) as waste. Facultative anaerobes can switch between fermentation and different terminal electron acceptors depending on the environmental conditions in which they find themselves.[110]

Growth and reproduction

Further information: Bacterial growth
drawing of showing the processes of binary fission, mitosis, and meiosis
Many bacteria reproduce through binary fission, which is compared to mitosis and meiosis in this image.
A culture of Salmonella
E. coli colony
A colony of Escherichia coli[111]

Unlike in multicellular organisms, increases in cell size (cell growth) and reproduction by cell division are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction.[112] Under optimal conditions, bacteria can grow and divide extremely rapidly, and some bacterial populations can double as quickly as every 17 minutes.[113] In cell division, two identical clone daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that help disperse the newly formed daughter cells. Examples include fruiting body formation by myxobacteria and aerial hyphae formation by Streptomyces species, or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell.[114]

In the laboratory, bacteria are usually grown using solid or liquid media.[115] Solid growth media, such as agar plates, are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when the measurement of growth or large volumes of cells are required. Growth in stirred liquid media occurs as an even cell suspension, making the cultures easy to divide and transfer, although isolating single bacteria from liquid media is difficult. The use of selective media (media with specific nutrients added or deficient, or with antibiotics added) can help identify specific organisms.[116]

Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly.[115] However, in natural environments, nutrients are limited, meaning that bacteria cannot continue to reproduce indefinitely. This nutrient limitation has led the evolution of different growth strategies (see r/K selection theory). Some organisms can grow extremely rapidly when nutrients become available, such as the formation of algal and cyanobacterial blooms that often occur in lakes during the summer.[117] Other organisms have adaptations to harsh environments, such as the production of multiple antibiotics by Streptomyces that inhibit the growth of competing microorganisms.[118] In nature, many organisms live in communities (e.g., biofilms) that may allow for increased supply of nutrients and protection from environmental stresses.[52] These relationships can be essential for growth of a particular organism or group of organisms (syntrophy).[119]

Bacterial growth follows four phases. When a population of bacteria first enter a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the lag phase, a period of slow growth when the cells are adapting to the high-nutrient environment and preparing for fast growth. The lag phase has high biosynthesis rates, as proteins necessary for rapid growth are produced.[120][121] The second phase of growth is the logarithmic phase, also known as the exponential phase. The log phase is marked by rapid exponential growth. The rate at which cells grow during this phase is known as the growth rate (k), and the time it takes the cells to double is known as the generation time (g). During log phase, nutrients are metabolised at maximum speed until one of the nutrients is depleted and starts limiting growth. The third phase of growth is the stationary phase and is caused by depleted nutrients. The cells reduce their metabolic activity and consume non-essential cellular proteins. The stationary phase is a transition from rapid growth to a stress response state and there is increased expression of genes involved in DNA repair, antioxidant metabolism and nutrient transport.[122] The final phase is the death phase where the bacteria run out of nutrients and die.[123]

Genetics

Main article: Bacterial genetics
Helium ion microscopy image showing T4 phage infecting E. coli. Some of the attached phage have contracted tails indicating that they have injected their DNA into the host. The bacterial cells are ~ 0.5 µm wide.[124]

Most bacteria have a single circular chromosome that can range in size from only 160,000 base pairs in the endosymbiotic bacteria Carsonella ruddii,[125] to 12,200,000 base pairs (12.2 Mbp) in the soil-dwelling bacteria Sorangium cellulosum.[126] There are many exceptions to this; for example, some Streptomyces and Borrelia species contain a single linear chromosome,[127][128] while some Vibrio species contain more than one chromosome.[129] Some bacteria contain plasmids, small extra-chromosomal molecules of DNA that may contain genes for various useful functions such as antibiotic resistance, metabolic capabilities, or various virulence factors.[130]

Bacteria genomes usually encode a few hundred to a few thousand genes. The genes in bacterial genomes are usually a single continuous stretch of DNA. Although several different types of introns do exist in bacteria, these are much rarer than in eukaryotes.[131]

Bacteria, as asexual organisms, inherit an identical copy of the parent's genome and are clonal. However, all bacteria can evolve by selection on changes to their genetic material DNA caused by genetic recombination or mutations. Mutations arise from errors made during the replication of DNA or from exposure to mutagens. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria.[132] Genetic changes in bacterial genomes emerge from either random mutation during replication or "stress-directed mutation", where genes involved in a particular growth-limiting process have an increased mutation rate.[133]

Some bacteria transfer genetic material between cells. This can occur in three main ways. First, bacteria can take up exogenous DNA from their environment in a process called transformation.[134] Many bacteria can naturally take up DNA from the environment, while others must be chemically altered in order to induce them to take up DNA.[135] The development of competence in nature is usually associated with stressful environmental conditions and seems to be an adaptation for facilitating repair of DNA damage in recipient cells.[136] Second, bacteriophages can integrate into the bacterial chromosome, introducing foreign DNA in a process known as transduction. Many types of bacteriophage exist; some infect and lyse their host bacteria, while others insert into the bacterial chromosome.[137] Bacteria resist phage infection through restriction modification systems that degrade foreign DNA,[138] and a system that uses CRISPR sequences to retain fragments of the genomes of phage that the bacteria have come into contact with in the past, which allows them to block virus replication through a form of RNA interference.[139][140] Third, bacteria can transfer genetic material through direct cell contact via conjugation.[141]

In ordinary circumstances, transduction, conjugation, and transformation involve transfer of DNA between individual bacteria of the same species, but occasionally transfer may occur between individuals of different bacterial species, and this may have significant consequences, such as the transfer of antibiotic resistance.[142][143] In such cases, gene acquisition from other bacteria or the environment is called horizontal gene transfer and may be common under natural conditions.[144]

Behaviour

Movement

Main article: Bacterial motility
Transmission electron micrograph of Desulfovibrio vulgaris showing a single flagellum at one end of the cell. Scale bar is 0.5 micrometers long.

Many bacteria are motile (able to move themselves) and do so using a variety of mechanisms. The best studied of these are flagella, long filaments that are turned by a motor at the base to generate propeller-like movement.[145] The bacterial flagellum is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly.[145] The flagellum is a rotating structure driven by a reversible motor at the base that uses the electrochemical gradient across the membrane for power.[146]

The different arrangements of bacterial flagella: A-Monotrichous; B-Lophotrichous; C-Amphitrichous; D-Peritrichous

Bacteria can use flagella in different ways to generate different kinds of movement. Many bacteria (such as E. coli) have two distinct modes of movement: forward movement (swimming) and tumbling. The tumbling allows them to reorient and makes their movement a three-dimensional random walk.[147] Bacterial species differ in the number and arrangement of flagella on their surface; some have a single flagellum (monotrichous), a flagellum at each end (amphitrichous), clusters of flagella at the poles of the cell (lophotrichous), while others have flagella distributed over the entire surface of the cell (peritrichous). The flagella of a unique group of bacteria, the spirochaetes, are found between two membranes in the periplasmic space. They have a distinctive helical body that twists about as it moves.[145]

Two other types of bacterial motion are called twitching motility that relies on a structure called the type IV pilus,[148] and gliding motility, that uses other mechanisms. In twitching motility, the rod-like pilus extends out from the cell, binds some substrate, and then retracts, pulling the cell forward.[149]

Motile bacteria are attracted or repelled by certain stimuli in behaviours called taxes: these include chemotaxis, phototaxis, energy taxis, and magnetotaxis.[150][151][152] In one peculiar group, the myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores.[47] The myxobacteria move only when on solid surfaces, unlike E. coli, which is motile in liquid or solid media.[153]

Several Listeria and Shigella species move inside host cells by usurping the cytoskeleton, which is normally used to move organelles inside the cell. By promoting actin polymerisation at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm.[154]

Communication

See also: Prokaryote § Sociality

A few bacteria have chemical systems that generate light. This bioluminescence often occurs in bacteria that live in association with fish, and the light probably serves to attract fish or other large animals.[155]

Bacteria often function as multicellular aggregates known as biofilms, exchanging a variety of molecular signals for intercell communication and engaging in coordinated multicellular behaviour.[156][157]

The communal benefits of multicellular cooperation include a cellular division of labour, accessing resources that cannot effectively be used by single cells, collectively defending against antagonists, and optimising population survival by differentiating into distinct cell types.[156] For example, bacteria in biofilms can have more than five hundred times increased resistance to antibacterial agents than individual "planktonic" bacteria of the same species.[157]

One type of intercellular communication by a molecular signal is called quorum sensing, which serves the purpose of determining whether the local population density is sufficient to support investment in processes that are only successful if large numbers of similar organisms behave similarly, such as excreting digestive enzymes or emitting light.[158][159] Quorum sensing enables bacteria to coordinate gene expression and to produce, release, and detect autoinducers or pheromones that accumulate with the growth in cell population.[160]

Classification and identification

Main article: Bacterial taxonomy
Further information: Scientific classification, Systematics, Bacterial phyla, and Clinical pathology
blue stain of Streptococcus mutans
Streptococcus mutans visualised with a Gram stain.
Phylogenetic tree showing the diversity of bacteria, compared to other organisms. Here bacteria are represented by three main supergroups: the CPR ultramicrobacterias, Terrabacteria and Gracilicutes according to recent genomic analyzes (2019).[161]

Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components, such as DNA, fatty acids, pigments, antigens and quinones.[116] While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species.[162] Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasises molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridisation, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene.[163] Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology,[164] and Bergey's Manual of Systematic Bacteriology.[165] The International Committee on Systematic Bacteriology (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in the International Code of Nomenclature of Bacteria.[166]

Historically, bacteria were considered a part of the Plantae, the Plant kingdom, and were called "Schizomycetes" (fission-fungi).[167] For this reason, collective bacteria and other microorganisms in a host are often called "flora".[168] The term "bacteria" was traditionally applied to all microscopic, single-cell prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor.[4] The archaea and eukaryotes are more closely related to each other than either is to the bacteria. These two domains, along with Eukarya, are the basis of the three-domain system, which is currently the most widely used classification system in microbiology.[169] However, due to the relatively recent introduction of molecular systematics and a rapid increase in the number of genome sequences that are available, bacterial classification remains a changing and expanding field.[170][171] For example, Cavalier-Smith argued that the Archaea and Eukaryotes evolved from Gram-positive bacteria.[172]

The identification of bacteria in the laboratory is particularly relevant in medicine, where the correct treatment is determined by the bacterial species causing an infection. Consequently, the need to identify human pathogens was a major impetus for the development of techniques to identify bacteria.[173]

The Gram stain, developed in 1884 by Hans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls.[174][74] The thick layers of peptidoglycan in the "Gram-positive" cell wall stain purple, while the thin "Gram-negative" cell wall appears pink.[174] By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci and Gram-negative bacilli). Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or Nocardia, which show acid fastness on Ziehl–Neelsen or similar stains.[175] Other organisms may need to be identified by their growth in special media, or by other techniques, such as serology.[176]

Culture techniques are designed to promote the growth and identify particular bacteria while restricting the growth of the other bacteria in the sample.[177] Often these techniques are designed for specific specimens; for example, a sputum sample will be treated to identify organisms that cause pneumonia, while stool specimens are cultured on selective media to identify organisms that cause diarrhea while preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, such as blood, urine or spinal fluid, are cultured under conditions designed to grow all possible organisms.[116][178] Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns (such as aerobic or anaerobic growth), patterns of hemolysis, and staining.[179]

As with bacterial classification, identification of bacteria is increasingly using molecular methods,[180] and mass spectroscopy.[181] Most bacteria have not been characterised and there are many species that cannot be grown in the laboratory.[182] Diagnostics using DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods.[183] These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing.[184] However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Following present classification, there are a little less than 9,300 known species of prokaryotes, which includes bacteria and archaea;[185] but attempts to estimate the true number of bacterial diversity have ranged from 107 to 109 total species—and even these diverse estimates may be off by many orders of magnitude.[186][187]

Phyla

Main article: Bacterial phyla

The following phyla have been validly published according to the Bacteriological Code:[188]

  • Acidobacteriota
  • Actinomycetota
  • Aquificota
  • Armatimonadota
  • Atribacterota
  • Bacillota
  • Bacteroidota
  • Balneolota
  • Bdellovibrionota
  • Caldisericota
  • Calditrichota
  • Campylobacterota
  • Chlamydiota
  • Chlorobiota
  • Chloroflexota
  • Chrysiogenota
  • Coprothermobacterota
  • Deferribacterota
  • Deinococcota
  • Dictyoglomota
  • Elusimicrobiota
  • Fibrobacterota
  • Fusobacteriota
  • Gemmatimonadota
  • Ignavibacteriota
  • Lentisphaerota
  • Mycoplasmatota
  • Myxococcota
  • Nitrospinota
  • Nitrospirota
  • Planctomycetota
  • Pseudomonadota
  • Rhodothermota
  • Spirochaetota
  • Synergistota
  • Thermodesulfobacteriota
  • Thermomicrobiota
  • Thermotogota
  • Verrucomicrobiota

Interactions with other organisms

Further information: Microbes in human culture
chart showing bacterial infections upon various parts of human body
Overview of bacterial infections and main species involved.[189]

Despite their apparent simplicity, bacteria can form complex associations with other organisms. These symbiotic associations can be divided into parasitism, mutualism and commensalism.[190]

Commensals

The word "commensalism" is derived from the word "commensal", meaning "eating at the same table"[191] and all plants and animals are colonised by commensal bacteria. In humans and other animals, millions of them live on the skin, the airways, the gut and other orifices.[192][193] Referred to as "normal flora",[194] or "commensals",[195] these bacteria usually cause no harm but may occasionally invade other sites of the body and cause infection. Escherichia coli is a commensal in the human gut but can cause urinary tract infections.[196] Similarly, streptococci, which are part of the normal flora of the human mouth, can cause heart disease.[197]

Predators

Some species of bacteria kill and then consume other microorganisms; these species are called predatory bacteria.[198] These include organisms such as Myxococcus xanthus, which forms swarms of cells that kill and digest any bacteria they encounter.[199] Other bacterial predators either attach to their prey in order to digest them and absorb nutrients or invade another cell and multiply inside the cytosol.[200] These predatory bacteria are thought to have evolved from saprophages that consumed dead microorganisms, through adaptations that allowed them to entrap and kill other organisms.[201]

Mutualists

Certain bacteria form close spatial associations that are essential for their survival. One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters of anaerobic bacteria that consume organic acids, such as butyric acid or propionic acid, and produce hydrogen, and methanogenic archaea that consume hydrogen.[202] The bacteria in this association are unable to consume the organic acids as this reaction produces hydrogen that accumulates in their surroundings. Only the intimate association with the hydrogen-consuming archaea keeps the hydrogen concentration low enough to allow the bacteria to grow.[203]

In soil, microorganisms that reside in the rhizosphere (a zone that includes the root surface and the soil that adheres to the root after gentle shaking) carry out nitrogen fixation, converting nitrogen gas to nitrogenous compounds.[204] This serves to provide an easily absorbable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found as symbionts in humans and other organisms. For example, the presence of over 1,000 bacterial species in the normal human gut flora of the intestines can contribute to gut immunity, synthesise vitamins, such as folic acid, vitamin K and biotin, convert sugars to lactic acid (see Lactobacillus), as well as fermenting complex undigestible carbohydrates.[205][206][207] The presence of this gut flora also inhibits the growth of potentially pathogenic bacteria (usually through competitive exclusion) and these beneficial bacteria are consequently sold as probiotic dietary supplements.[208]

Nearly all animal life is dependent on bacteria for survival as only bacteria and some archaea possess the genes and enzymes necessary to synthesize vitamin B12, also known as cobalamin, and provide it through the food chain. Vitamin B12 is a water-soluble vitamin that is involved in the metabolism of every cell of the human body. It is a cofactor in DNA synthesis and in both fatty acid and amino acid metabolism. It is particularly important in the normal functioning of the nervous system via its role in the synthesis of myelin.[209]

Pathogens

Main article: Pathogenic bacteria
Neisseria gonorrhoeae and pus cells from a penile discharge (Gram stain)
Color-enhanced scanning electron micrograph of red Salmonella typhimurium in yellow human cells
Colour-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells

The body is continually exposed to many species of bacteria, including beneficial commensals, which grow on the skin and mucous membranes, and saprophytes, which grow mainly in the soil and in decaying matter. The blood and tissue fluids contain nutrients sufficient to sustain the growth of many bacteria. The body has defence mechanisms that enable it to resist microbial invasion of its tissues and give it a natural immunity or innate resistance against many microorganisms.[210] Unlike some viruses, bacteria evolve relatively slowly so many bacterial diseases also occur in other animals.[211]

If bacteria form a parasitic association with other organisms, they are classed as pathogens.[212] Pathogenic bacteria are a major cause of human death and disease and cause infections such as tetanus (caused by Clostridium tetani), typhoid fever, diphtheria, syphilis, cholera, foodborne illness, leprosy (caused by Mycobacterium leprae) and tuberculosis (caused by Mycobacterium tuberculosis).[213] A pathogenic cause for a known medical disease may only be discovered many years later, as was the case with Helicobacter pylori and peptic ulcer disease.[214] Bacterial diseases are also important in agriculture, and bacteria cause leaf spot, fire blight and wilts in plants, as well as Johne's disease, mastitis, salmonella and anthrax in farm animals.[215]

Gram-stained micrograph of bacteria from the vagina
In bacterial vaginosis, beneficial bacteria in the vagina (top) are displaced by pathogens (bottom). Gram stain.

Each species of pathogen has a characteristic spectrum of interactions with its human hosts. Some organisms, such as Staphylococcus or Streptococcus, can cause skin infections, pneumonia, meningitis and sepsis, a systemic inflammatory response producing shock, massive vasodilation and death.[216] Yet these organisms are also part of the normal human flora and usually exist on the skin or in the nose without causing any disease at all. Other organisms invariably cause disease in humans, such as Rickettsia, which are obligate intracellular parasites able to grow and reproduce only within the cells of other organisms. One species of Rickettsia causes typhus, while another causes Rocky Mountain spotted fever. Chlamydia, another phylum of obligate intracellular parasites, contains species that can cause pneumonia or urinary tract infection and may be involved in coronary heart disease.[217] Some species, such as Pseudomonas aeruginosa, Burkholderia cenocepacia, and Mycobacterium avium, are opportunistic pathogens and cause disease mainly in people who are immunosuppressed or have cystic fibrosis.[218][219] Some bacteria produce toxins, which cause diseases.[220] These are endotoxins, which come from broken bacterial cells, and exotoxins, which are produced by bacteria and released into the environment.[221] The bacterium Clostridium botulinum for example, produces a powerful exotoxin that cause respiratory paralysis, and Salmonellae produce an endotoxin that causes gastroenteritis.[221] Some exotoxins can be converted to toxoids, which are used as vaccines to prevent the disease.[222]

Bacterial infections may be treated with antibiotics, which are classified as bacteriocidal if they kill bacteria or bacteriostatic if they just prevent bacterial growth. There are many types of antibiotics, and each class inhibits a process that is different in the pathogen from that found in the host. An example of how antibiotics produce selective toxicity are chloramphenicol and puromycin, which inhibit the bacterial ribosome, but not the structurally different eukaryotic ribosome.[223] Antibiotics are used both in treating human disease and in intensive farming to promote animal growth, where they may be contributing to the rapid development of antibiotic resistance in bacterial populations.[224] Infections can be prevented by antiseptic measures such as sterilising the skin prior to piercing it with the needle of a syringe, and by proper care of indwelling catheters. Surgical and dental instruments are also sterilised to prevent contamination by bacteria. Disinfectants such as bleach are used to kill bacteria or other pathogens on surfaces to prevent contamination and further reduce the risk of infection.[225]

Significance in technology and industry

Bacteria, often lactic acid bacteria, such as Lactobacillus species and Lactococcus species, in combination with yeasts and moulds, have been used for thousands of years in the preparation of fermented foods, such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine, and yogurt.[226][227]

The ability of bacteria to degrade a variety of organic compounds is remarkable and has been used in waste processing and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills.[228] Fertiliser was added to some of the beaches in Prince William Sound in an attempt to promote the growth of these naturally occurring bacteria after the 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were not too thickly covered in oil. Bacteria are also used for the bioremediation of industrial toxic wastes.[229] In the chemical industry, bacteria are most important in the production of enantiomerically pure chemicals for use as pharmaceuticals or agrichemicals.[230]

Bacteria can also be used in place of pesticides in biological pest control. This commonly involves Bacillus thuringiensis (also called BT), a Gram-positive, soil-dwelling bacterium. Subspecies of this bacteria are used as Lepidopteran-specific insecticides under trade names such as Dipel and Thuricide.[231] Because of their specificity, these pesticides are regarded as environmentally friendly, with little or no effect on humans, wildlife, pollinators, and most other beneficial insects.[232][233]

Because of their ability to quickly grow and the relative ease with which they can be manipulated, bacteria are the workhorses for the fields of molecular biology, genetics, and biochemistry. By making mutations in bacterial DNA and examining the resulting phenotypes, scientists can determine the function of genes, enzymes, and metabolic pathways in bacteria, then apply this knowledge to more complex organisms.[234] This aim of understanding the biochemistry of a cell reaches its most complex expression in the synthesis of huge amounts of enzyme kinetic and gene expression data into mathematical models of entire organisms. This is achievable in some well-studied bacteria, with models of Escherichia coli metabolism now being produced and tested.[235][236] This understanding of bacterial metabolism and genetics allows the use of biotechnology to bioengineer bacteria for the production of therapeutic proteins, such as insulin, growth factors, or antibodies.[237][238]

Because of their importance for research in general, samples of bacterial strains are isolated and preserved in Biological Resource Centers. This ensures the availability of the strain to scientists worldwide.[239]

History of bacteriology

For the history of microbiology, see Microbiology. For the history of bacterial classification, see Bacterial taxonomy. For the natural history of Bacteria, see Last universal common ancestor.
painting of Antonie van Leeuwenhoek, in robe and frilled shirt, with ink pen and paper
Antonie van Leeuwenhoek, the first microbiologist and the first person to observe bacteria using a microscope.

Bacteria were first observed by the Dutch microscopist Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design. He then published his observations in a series of letters to the Royal Society of London.[240] Bacteria were Leeuwenhoek's most remarkable microscopic discovery. Their size was just at the limit of what his simple lenses could resolve, and, in one of the most striking hiatuses in the history of science, no one else would see them again for over a century.[241] His observations also included protozoans which he called animalcules, and his findings were looked at again in the light of the more recent findings of cell theory.[242]

Christian Gottfried Ehrenberg introduced the word "bacterium" in 1828.[243] In fact, his Bacterium was a genus that contained non-spore-forming rod-shaped bacteria,[244] as opposed to Bacillus, a genus of spore-forming rod-shaped bacteria defined by Ehrenberg in 1835.[245]

Louis Pasteur demonstrated in 1859 that the growth of microorganisms causes the fermentation process and that this growth is not due to spontaneous generation (yeasts and molds, commonly associated with fermentation, are not bacteria, but rather fungi). Along with his contemporary Robert Koch, Pasteur was an early advocate of the germ theory of disease.[246] Before them, Ignaz Semmelweis and Joseph Lister had realised the importance of sanitized hands in medical work. Semmelweis, who in the 1840s formulated his rules for handwashing in the hospital, prior to the advent of germ theory, attributed disease to "decomposing animal organic matter." His ideas were rejected and his book on the topic condemned by the medical community. After Lister, however, doctors started sanitizing their hands in the 1870s.[247]

Robert Koch, a pioneer in medical microbiology, worked on cholera, anthrax and tuberculosis. In his research into tuberculosis, Koch finally proved the germ theory, for which he received a Nobel Prize in 1905.[248] In Koch's postulates, he set out criteria to test if an organism is the cause of a disease, and these postulates are still used today.[249]

Ferdinand Cohn is said to be a founder of bacteriology, studying bacteria from 1870. Cohn was the first to classify bacteria based on their morphology.[250][251]

Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available.[252] In 1910, Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained Treponema pallidum—the spirochaete that causes syphilis—into compounds that selectively killed the pathogen.[253] Ehrlich, who had been awarded a 1908 Nobel Prize for his work on immunology, pioneered the use of stains to detect and identify bacteria, with his work being the basis of the Gram stain and the Ziehl–Neelsen stain.[254]

A major step forward in the study of bacteria came in 1977 when Carl Woese recognised that archaea have a separate line of evolutionary descent from bacteria.[255] This new phylogenetic taxonomy depended on the sequencing of 16S ribosomal RNA and divided prokaryotes into two evolutionary domains, as part of the three-domain system.[4]

See also

  • Bacteriohopanepolyol
  • Genetically modified bacteria
  • Marine prokaryotes

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Bibliography

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External links

  • On-line text book on bacteriology (2015)
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Prokaryotes: Bacteria classification
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Archaea
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Eukaryota
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Diaphoretickes
Plant
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Alveolata
Rhizaria
Amorphea
Amoebozoa
Opisthokonta
Animal
Fungi)
Terrabacteria
BV1, BV3, BV5
others
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    • Acidimicrobiia
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    • "Aquicultoria"
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    • "Geothermincolia"
    • "Humimicrobiia"
    • Rubrobacteria
    • Thermoleophilia
  • "Bipolaricaulota"
    • "Bipolaricaulia"
  • Chloroflexota
    • "Caldilineia"
    • Chloroflexia
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    • Ktedonobacteria
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  • Deinococcota
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    • Armatimonadia
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    • "Eremiobacteria"
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BV3
Low GC
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(Planctobacteria)
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(Sphingobacteria)
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    • Chlorobiia
    • "Ignavibacteriia"
    • "Kapabacteria"
    • "Kryptoniia"
    • Rhodothermia
  • Calditrichota
    • Calditrichia
  • "Cloacimonadota"
    • "Cloacimonadia"
  • "Coatesbacteria"
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  • "Eisenbacteria"
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    • "Heilongiia"
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    • "Stahlbacteria"
  • "Krumholzibacteriota"
    • "Krumholzibacteriia"
  • "Latescibacteria"
    • "Handelsmanbacteria"
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    • "Marinisomatia"
  • "Tianyabacteria"
  • "Zixibacteria"
Proteobacteria
BV2
Aquificida
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    • "Acidulodesulfobacteriia"
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    • "Thermosulfidibacteria"
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  • "Deferrisomatota"
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    • Desulfuromonadia
  • "Desulfobacterota"
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    • "Lernaellia"
  • "Methylomirabilota"
    • "Methylomirabilia"
  • "Modulibacteria"
    • "Moduliflexia"
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    • "Bradymonadia"
    • Polyangiia
  • Nitrospinota
    • Nitrospinia
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    • Nitrospiria
    • "Thermodesulfovibrionia"
  • SAR324
    • "Lambdaproteobacteria"
  • "Schekmanbacteria"
  • "Tectomicrobia"
    • "Entotheonellia"
others
  • Acidobacteriota
    • "Acidobacteriia"
    • "Aminicenantia"
    • Blastocatellia
    • "Fischerbacteria"
    • "Guanabaribacteriia"
    • "Holophagia"
    • "Polarisedimenticolia"
    • Thermoanaerobaculia
    • Vicinamibacteria
  • "Canglongiota"
    • "Canglongiia"
  • "Leptospirillaeota"
    • "Leptospirillia"
  • Pseudomonadota
    • "Caulobacteria"
    • "Mariprofundia"
    • "Magnetococcia"
    • "Pseudomonadia"
others
  • "Qinglongiota"
    • "Qinglongiia"
  • "Salinosulfoleibacteria"
  • "Teskebacteria"
  • Source: Bergey's Manual (2001–2012)
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From Wikipedia, the free encyclopedia
(Redirected from Microbial life)
Microscopic living organism
"Microbe" redirects here. For other uses, see Microbe (disambiguation).

A cluster of Escherichia coli bacteria magnified 10,000 times
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A microorganism, or microbe,[a] is an organism of microscopic size, which may exist in its single-celled form or as a colony of cells.

The possible existence of unseen microbial life was suspected from ancient times, such as in Jain scriptures from sixth century BC India. The scientific study of microorganisms began with their observation under the microscope in the 1670s by Anton van Leeuwenhoek. In the 1850s, Louis Pasteur found that microorganisms caused food spoilage, debunking the theory of spontaneous generation. In the 1880s, Robert Koch discovered that microorganisms caused the diseases tuberculosis, cholera, diphtheria, and anthrax.

Because microorganisms include most unicellular organisms from all three domains of life they can be extremely diverse. Two of the three domains, Archaea and Bacteria, only contain microorganisms. The third domain Eukaryota includes all multicellular organisms as well as many unicellular protists and protozoans that are microbes. Some protists are related to animals and some to green plants. There are also many multicellular organisms that are microscopic, namely micro-animals, some fungi, and some algae, but these are generally not considered microorganisms.[further explanation needed]

Microorganisms can have very different habitats, and live everywhere from the poles to the equator, deserts, geysers, rocks, and the deep sea. Some are adapted to extremes such as very hot or very cold conditions, others to high pressure, and a few, such as Deinococcus radiodurans, to high radiation environments. Microorganisms also make up the microbiota found in and on all multicellular organisms. There is evidence that 3.45-billion-year-old Australian rocks once contained microorganisms, the earliest direct evidence of life on Earth.[1][2]

Microbes are important in human culture and health in many ways, serving to ferment foods and treat sewage, and to produce fuel, enzymes, and other bioactive compounds. Microbes are essential tools in biology as model organisms and have been put to use in biological warfare and bioterrorism. Microbes are a vital component of fertile soil. In the human body, microorganisms make up the human microbiota, including the essential gut flora. The pathogens responsible for many infectious diseases are microbes and, as such, are the target of hygiene measures.

Discovery[edit]

See also: History of biology and Microbiology § History

Ancient precursors[edit]

Mahavira postulated the existence of microscopic creatures in the 6th century BC
Antonie van Leeuwenhoek was the first to study microscopic organisms.
Lazzaro Spallanzani showed that boiling a broth stopped it from decaying.

The possible existence of microscopic organisms was discussed for many centuries before their discovery in the seventeenth century. By the 6th century BC, the Jains of present-day India postulated the existence of tiny organisms called nigodas.[3] These nigodas are said to be born in clusters; they live everywhere, including the bodies of plants, animals, and people; and their life lasts only for a fraction of a second.[4] According to Mahavira, the 24th preacher of Jainism, the humans destroy these nigodas on a massive scale, when they eat, breathe, sit, and move.[3] Many modern Jains assert that Mahavira's teachings presage the existence of microorganisms as discovered by modern science.[5]

The earliest known idea to indicate the possibility of diseases spreading by yet unseen organisms was that of the Roman scholar Marcus Terentius Varro in a first-century BC book entitled On Agriculture in which he called the unseen creatures animalia minuta, and warns against locating a homestead near a swamp:[6]

… and because there are bred certain minute creatures that cannot be seen by the eyes, which float in the air and enter the body through the mouth and nose and they cause serious diseases.[6]

In The Canon of Medicine (1020), Avicenna suggested that tuberculosis and other diseases might be contagious.[7][8]

Early modern[edit]

Further information: Microscopic discovery of bacteria

Akshamsaddin (Turkish scientist) mentioned the microbe in his work Maddat ul-Hayat (The Material of Life) about two centuries prior to Antonie van Leeuwenhoek's discovery through experimentation:

It is incorrect to assume that diseases appear one by one in humans. Disease infects by spreading from one person to another. This infection occurs through seeds that are so small they cannot be seen but are alive.[9][10]

In 1546, Girolamo Fracastoro proposed that epidemic diseases were caused by transferable seedlike entities that could transmit infection by direct or indirect contact, or even without contact over long distances.[11]

Antonie van Leeuwenhoek is considered to be one of the fathers of microbiology. He was the first in 1673 to discover and conduct scientific experiments with microorganisms, using simple single-lensed microscopes of his own design.[12][13][14][15] Robert Hooke, a contemporary of Leeuwenhoek, also used microscopy to observe microbial life in the form of the fruiting bodies of moulds. In his 1665 book Micrographia, he made drawings of studies, and he coined the term cell.[16]

19th century[edit]

Louis Pasteur showed that Spallanzani's findings held even if air could enter through a filter that kept particles out.

Louis Pasteur (1822–1895) exposed boiled broths to the air, in vessels that contained a filter to prevent particles from passing through to the growth medium, and also in vessels without a filter, but with air allowed in via a curved tube so dust particles would settle and not come in contact with the broth. By boiling the broth beforehand, Pasteur ensured that no microorganisms survived within the broths at the beginning of his experiment. Nothing grew in the broths in the course of Pasteur's experiment. This meant that the living organisms that grew in such broths came from outside, as spores on dust, rather than spontaneously generated within the broth. Thus, Pasteur refuted the theory of spontaneous generation and supported the germ theory of disease.[17]

Robert Koch showed that microorganisms caused disease.

In 1876, Robert Koch (1843–1910) established that microorganisms can cause disease. He found that the blood of cattle that were infected with anthrax always had large numbers of Bacillus anthracis. Koch found that he could transmit anthrax from one animal to another by taking a small sample of blood from the infected animal and injecting it into a healthy one, and this caused the healthy animal to become sick. He also found that he could grow the bacteria in a nutrient broth, then inject it into a healthy animal, and cause illness. Based on these experiments, he devised criteria for establishing a causal link between a microorganism and a disease and these are now known as Koch's postulates.[18] Although these postulates cannot be applied in all cases, they do retain historical importance to the development of scientific thought and are still being used today.[19]

The discovery of microorganisms such as Euglena that did not fit into either the animal or plant kingdoms, since they were photosynthetic like plants, but motile like animals, led to the naming of a third kingdom in the 1860s. In 1860 John Hogg called this the Protoctista, and in 1866 Ernst Haeckel named it the Protista.[20][21][22]

The work of Pasteur and Koch did not accurately reflect the true diversity of the microbial world because of their exclusive focus on microorganisms having direct medical relevance. It was not until the work of Martinus Beijerinck and Sergei Winogradsky late in the nineteenth century that the true breadth of microbiology was revealed.[23] Beijerinck made two major contributions to microbiology: the discovery of viruses and the development of enrichment culture techniques.[24] While his work on the tobacco mosaic virus established the basic principles of virology, it was his development of enrichment culturing that had the most immediate impact on microbiology by allowing for the cultivation of a wide range of microbes with wildly different physiologies. Winogradsky was the first to develop the concept of chemolithotrophy and to thereby reveal the essential role played by microorganisms in geochemical processes.[25] He was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria.[23] French-Canadian microbiologist Felix d'Herelle co-discovered bacteriophages and was one of the earliest applied microbiologists.[26]

Classification and structure[edit]

Microorganisms can be found almost anywhere on Earth. Bacteria and archaea are almost always microscopic, while a number of eukaryotes are also microscopic, including most protists, some fungi, as well as some micro-animals and plants. Viruses are generally regarded as not living and therefore not considered to be microorganisms, although a subfield of microbiology is virology, the study of viruses.[27][28][29]

Evolution[edit]

Further information: Timeline of evolution and Earliest known life forms
BacteriaArchaeaEukaryotaAquifexThermotogaBacteroides–CytophagaPlanctomyces"Cyanobacteria"ProteobacteriaSpirochetesGram-positivesChloroflexiThermoproteus–PyrodictiumThermococcus celerMethanococcusMethanobacteriumMethanosarcinaHaloarchaeaEntamoebaeSlime moldsAnimalsFungiPlantsCiliatesFlagellatesTrichomonadsMicrosporidiaDiplomonads
Carl Woese's 1990 phylogenetic tree based on rRNA data shows the domains of Bacteria, Archaea, and Eukaryota. All are microorganisms except some eukaryote groups.

Single-celled microorganisms were the first forms of life to develop on Earth, approximately 3.5 billion years ago.[30][31][32] Further evolution was slow,[33] and for about 3 billion years in the Precambrian eon, (much of the history of life on Earth), all organisms were microorganisms.[34][35] Bacteria, algae and fungi have been identified in amber that is 220 million years old, which shows that the morphology of microorganisms has changed little since at least the Triassic period.[36] The newly discovered biological role played by nickel, however – especially that brought about by volcanic eruptions from the Siberian Traps – may have accelerated the evolution of methanogens towards the end of the Permian–Triassic extinction event.[37]

Microorganisms tend to have a relatively fast rate of evolution. Most microorganisms can reproduce rapidly, and bacteria are also able to freely exchange genes through conjugation, transformation and transduction, even between widely divergent species.[38] This horizontal gene transfer, coupled with a high mutation rate and other means of transformation, allows microorganisms to swiftly evolve (via natural selection) to survive in new environments and respond to environmental stresses. This rapid evolution is important in medicine, as it has led to the development of multidrug resistant pathogenic bacteria, superbugs, that are resistant to antibiotics.[39]

A possible transitional form of microorganism between a prokaryote and a eukaryote was discovered in 2012 by Japanese scientists. Parakaryon myojinensis is a unique microorganism larger than a typical prokaryote, but with nuclear material enclosed in a membrane as in a eukaryote, and the presence of endosymbionts. This is seen to be the first plausible evolutionary form of microorganism, showing a stage of development from the prokaryote to the eukaryote.[40][41]

Archaea[edit]

Main article: Archaea
Further information: Prokaryote

Archaea are prokaryotic unicellular organisms, and form the first domain of life in Carl Woese's three-domain system. A prokaryote is defined as having no cell nucleus or other membrane bound-organelle. Archaea share this defining feature with the bacteria with which they were once grouped. In 1990 the microbiologist Woese proposed the three-domain system that divided living things into bacteria, archaea and eukaryotes,[42] and thereby split the prokaryote domain.

Archaea differ from bacteria in both their genetics and biochemistry. For example, while bacterial cell membranes are made from phosphoglycerides with ester bonds, archaean membranes are made of ether lipids.[43] Archaea were originally described as extremophiles living in extreme environments, such as hot springs, but have since been found in all types of habitats.[44] Only now are scientists beginning to realize how common archaea are in the environment, with Thermoproteota (formerly Crenarchaeota) being the most common form of life in the ocean, dominating ecosystems below 150 m in depth.[45][46] These organisms are also common in soil and play a vital role in ammonia oxidation.[47]

The combined domains of archaea and bacteria make up the most diverse and abundant group of organisms on Earth and inhabit practically all environments where the temperature is below +140 °C. They are found in water, soil, air, as the microbiome of an organism, hot springs and even deep beneath the Earth's crust in rocks.[48] The number of prokaryotes is estimated to be around five nonillion, or 5 × 1030, accounting for at least half the biomass on Earth.[49]

The biodiversity of the prokaryotes is unknown, but may be very large. A May 2016 estimate, based on laws of scaling from known numbers of species against the size of organism, gives an estimate of perhaps 1 trillion species on the planet, of which most would be microorganisms. Currently, only one-thousandth of one percent of that total have been described.[50] Archael cells of some species aggregate and transfer DNA from one cell to another through direct contact, particularly under stressful environmental conditions that cause DNA damage.[51][52]

Bacteria[edit]

Main article: Bacteria
Staphylococcus aureus bacteria magnified about 10,000x

Bacteria like archaea are prokaryotic – unicellular, and having no cell nucleus or other membrane-bound organelle. Bacteria are microscopic, with a few extremely rare exceptions, such as Thiomargarita namibiensis.[53] Bacteria function and reproduce as individual cells, but they can often aggregate in multicellular colonies.[54] Some species such as myxobacteria can aggregate into complex swarming structures, operating as multicellular groups as part of their life cycle,[55] or form clusters in bacterial colonies such as E.coli.

Their genome is usually a circular bacterial chromosome – a single loop of DNA, although they can also harbor small pieces of DNA called plasmids. These plasmids can be transferred between cells through bacterial conjugation. Bacteria have an enclosing cell wall, which provides strength and rigidity to their cells. They reproduce by binary fission or sometimes by budding, but do not undergo meiotic sexual reproduction. However, many bacterial species can transfer DNA between individual cells by a horizontal gene transfer process referred to as natural transformation.[56] Some species form extraordinarily resilient spores, but for bacteria this is a mechanism for survival, not reproduction. Under optimal conditions bacteria can grow extremely rapidly and their numbers can double as quickly as every 20 minutes.[57]

Eukaryotes[edit]

Main article: Eukaryote

Most living things that are visible to the naked eye in their adult form are eukaryotes, including humans. However, many eukaryotes are also microorganisms. Unlike bacteria and archaea, eukaryotes contain organelles such as the cell nucleus, the Golgi apparatus and mitochondria in their cells. The nucleus is an organelle that houses the DNA that makes up a cell's genome. DNA (Deoxyribonucleic acid) itself is arranged in complex chromosomes.[58] Mitochondria are organelles vital in metabolism as they are the site of the citric acid cycle and oxidative phosphorylation. They evolved from symbiotic bacteria and retain a remnant genome.[59] Like bacteria, plant cells have cell walls, and contain organelles such as chloroplasts in addition to the organelles in other eukaryotes. Chloroplasts produce energy from light by photosynthesis, and were also originally symbiotic bacteria.[59]

Unicellular eukaryotes consist of a single cell throughout their life cycle. This qualification is significant since most multicellular eukaryotes consist of a single cell called a zygote only at the beginning of their life cycles. Microbial eukaryotes can be either haploid or diploid, and some organisms have multiple cell nuclei.[60]

Unicellular eukaryotes usually reproduce asexually by mitosis under favorable conditions. However, under stressful conditions such as nutrient limitations and other conditions associated with DNA damage, they tend to reproduce sexually by meiosis and syngamy.[61]

Protists[edit]

Main article: Protista
Euglena mutabilis, a photosynthetic flagellate

Of eukaryotic groups, the protists are most commonly unicellular and microscopic. This is a highly diverse group of organisms that are not easy to classify.[62][63] Several algae species are multicellular protists, and slime molds have unique life cycles that involve switching between unicellular, colonial, and multicellular forms.[64] The number of species of protists is unknown since only a small proportion has been identified. Protist diversity is high in oceans, deep sea-vents, river sediment and an acidic river, suggesting that many eukaryotic microbial communities may yet be discovered.[65][66]

Fungi[edit]

Main article: Fungus

The fungi have several unicellular species, such as baker's yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe). Some fungi, such as the pathogenic yeast Candida albicans, can undergo phenotypic switching and grow as single cells in some environments, and filamentous hyphae in others.[67]

Plants[edit]

Main article: Plant

The green algae are a large group of photosynthetic eukaryotes that include many microscopic organisms. Although some green algae are classified as protists, others such as charophyta are classified with embryophyte plants, which are the most familiar group of land plants. Algae can grow as single cells, or in long chains of cells. The green algae include unicellular and colonial flagellates, usually but not always with two flagella per cell, as well as various colonial, coccoid, and filamentous forms. In the Charales, which are the algae most closely related to higher plants, cells differentiate into several distinct tissues within the organism. There are about 6000 species of green algae.[68]

Ecology[edit]

Main article: Microbial ecology

Microorganisms are found in almost every habitat present in nature, including hostile environments such as the North and South poles, deserts, geysers, and rocks. They also include all the marine microorganisms of the oceans and deep sea. Some types of microorganisms have adapted to extreme environments and sustained colonies; these organisms are known as extremophiles. Extremophiles have been isolated from rocks as much as 7 kilometres below the Earth's surface,[69] and it has been suggested that the amount of organisms living below the Earth's surface is comparable with the amount of life on or above the surface.[48] Extremophiles have been known to survive for a prolonged time in a vacuum, and can be highly resistant to radiation, which may even allow them to survive in space.[70] Many types of microorganisms have intimate symbiotic relationships with other larger organisms; some of which are mutually beneficial (mutualism), while others can be damaging to the host organism (parasitism). If microorganisms can cause disease in a host they are known as pathogens and then they are sometimes referred to as microbes. Microorganisms play critical roles in Earth's biogeochemical cycles as they are responsible for decomposition and nitrogen fixation.[71]

Bacteria use regulatory networks that allow them to adapt to almost every environmental niche on earth.[72][73] A network of interactions among diverse types of molecules including DNA, RNA, proteins and metabolites, is utilised by the bacteria to achieve regulation of gene expression. In bacteria, the principal function of regulatory networks is to control the response to environmental changes, for example nutritional status and environmental stress.[74] A complex organization of networks permits the microorganism to coordinate and integrate multiple environmental signals.[72]

Extremophiles[edit]

Main article: Extremophile
Further information: List of microorganisms tested in outer space
A tetrad of Deinococcus radiodurans, a radioresistant extremophile bacterium

Extremophiles are microorganisms that have adapted so that they can survive and even thrive in extreme environments that are normally fatal to most life-forms. Thermophiles and hyperthermophiles thrive in high temperatures. Psychrophiles thrive in extremely low temperatures. – Temperatures as high as 130 °C (266 °F),[75] as low as −17 °C (1 °F)[76] Halophiles such as Halobacterium salinarum (an archaean) thrive in high salt conditions, up to saturation.[77] Alkaliphiles thrive in an alkaline pH of about 8.5–11.[78] Acidophiles can thrive in a pH of 2.0 or less.[79] Piezophiles thrive at very high pressures: up to 1,000–2,000 atm, down to 0 atm as in a vacuum of space.[80] A few extremophiles such as Deinococcus radiodurans are radioresistant,[81] resisting radiation exposure of up to 5k Gy. Extremophiles are significant in different ways. They extend terrestrial life into much of the Earth's hydrosphere, crust and atmosphere, their specific evolutionary adaptation mechanisms to their extreme environment can be exploited in biotechnology, and their very existence under such extreme conditions increases the potential for extraterrestrial life.[82]

Plants and Soil[edit]

Main article: Soil biology

The nitrogen cycle in soils depends on the fixation of atmospheric nitrogen. This is achieved by a number of diazotrophs. One way this can occur is in the root nodules of legumes that contain symbiotic bacteria of the genera Rhizobium, Mesorhizobium, Sinorhizobium, Bradyrhizobium, and Azorhizobium.[83]

The roots of plants create a narrow region known as the rhizosphere that supports many microorganisms known as the root microbiome.[84]

These microorganisms in the root microbiome are able to interact with each other and surrounding plants through signals and cues. For example, mycorrhizal fungi are able to communicate with the root systems of many plants through chemical signals between both the plant and fungi. This results in a mutualistic symbiosis between the two. However, these signals can be eavesdropped by other microorganisms, such as the soil bacteria, Myxococcus xanthus, which preys on other bacteria. Eavesdropping, or the interception of signals from unintended receivers, such as plants and microorganisms, can lead to large-scale, evolutionary consequences. For example, signaler-receiver pairs, like plant-microorganism pairs, may lose the ability to communicate with neighboring populations because of variability in eavesdroppers. In adapting to avoid local eavesdroppers, signal divergence could occur and thus, lead to the isolation of plants and microorganisms from the inability to communicate with other populations.[85]

Symbiosis[edit]

The photosynthetic cyanobacterium Hyella caespitosa (round shapes) with fungal hyphae (translucent threads) in the lichen Pyrenocollema halodytes

A lichen is a symbiosis of a macroscopic fungus with photosynthetic microbial algae or cyanobacteria.[86][87]

Applications[edit]

Main article: Human interactions with microbes

Microorganisms are useful in producing foods, treating waste water, creating biofuels and a wide range of chemicals and enzymes. They are invaluable in research as model organisms. They have been weaponised and sometimes used in warfare and bioterrorism. They are vital to agriculture through their roles in maintaining soil fertility and in decomposing organic matter.

Food production[edit]

Main articles: Fermentation in food processing and Food microbiology

Microorganisms are used in a fermentation process to make yoghurt, cheese, curd, kefir, ayran, xynogala, and other types of food. Fermentation cultures provide flavour and aroma, and inhibit undesirable organisms.[88] They are used to leaven bread, and to convert sugars to alcohol in wine and beer. Microorganisms are used in brewing, wine making, baking, pickling and other food-making processes.[89]

Some industrial uses of Microorganisms:

Product Contribution of Microorganisms
Cheese Growth of microorganisms contributes to ripening and flavor. The flavor and appearance of a particular cheese is due in large part to the microorganisms associated with it. Lactobacillus Bulgaricus is one of the microbes used in production of dairy products
Alcoholic beverages yeast is used to convert sugar, grape juice, or malt-treated grain into alcohol. other microorganisms may also be used; a mold converts starch into sugar to make the Japanese rice wine, sake. Acetobacter Aceti a kind of bacterium is used in production of Alcoholic beverages
Vinegar Certain bacteria are used to convert alcohol into acetic acid, which gives vinegar its acid taste. Acetobacter Aceti is used on production of vinegar, which gives vinegar odor of alcohol and alcoholic taste
Citric acid Certain fungi are used to make citric acid, a common ingredient of soft drinks and other foods.
Vitamins Microorganisms are used to make vitamins, including C, B2 , B12.
Antibiotics With only a few exceptions, microorganisms are used to make antibiotics. Penicillin, Amoxicillin, Tetracycline, and Erythromycin

Water treatment[edit]

Further information: Drinking water § Water quality
Wastewater treatment plants rely largely on microorganisms to oxidise organic matter.

These depend for their ability to clean up water contaminated with organic material on microorganisms that can respire dissolved substances. Respiration may be aerobic, with a well-oxygenated filter bed such as a slow sand filter.[90] Anaerobic digestion by methanogens generate useful methane gas as a by-product.[91]

Energy[edit]

Microorganisms are used in fermentation to produce ethanol,[92] and in biogas reactors to produce methane.[93] Scientists are researching the use of algae to produce liquid fuels,[94] and bacteria to convert various forms of agricultural and urban waste into usable fuels.[95]

Chemicals, enzymes[edit]

Further information: Synthesis of nanoparticles by fungi

Microorganisms are used to produce many commercial and industrial chemicals, enzymes and other bioactive molecules. Organic acids produced on a large industrial scale by microbial fermentation include acetic acid produced by acetic acid bacteria such as Acetobacter aceti, butyric acid made by the bacterium Clostridium butyricum, lactic acid made by Lactobacillus and other lactic acid bacteria,[96] and citric acid produced by the mould fungus Aspergillus niger.[96]

Microorganisms are used to prepare bioactive molecules such as Streptokinase from the bacterium Streptococcus,[97] Cyclosporin A from the ascomycete fungus Tolypocladium inflatum,[98] and statins produced by the yeast Monascus purpureus.[99]

Science[edit]

See also: Genetically modified bacteria
A laboratory fermentation vessel

Microorganisms are essential tools in biotechnology, biochemistry, genetics, and molecular biology. The yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe are important model organisms in science, since they are simple eukaryotes that can be grown rapidly in large numbers and are easily manipulated.[100] They are particularly valuable in genetics, genomics and proteomics.[101][102] Microorganisms can be harnessed for uses such as creating steroids and treating skin diseases. Scientists are also considering using microorganisms for living fuel cells,[103] and as a solution for pollution.[104]

Warfare[edit]

Main articles: Biological warfare and Bioterrorism

In the Middle Ages, as an early example of biological warfare, diseased corpses were thrown into castles during sieges using catapults or other siege engines. Individuals near the corpses were exposed to the pathogen and were likely to spread that pathogen to others.[105]

In modern times, bioterrorism has included the 1984 Rajneeshee bioterror attack[106] and the 1993 release of anthrax by Aum Shinrikyo in Tokyo.[107]

Soil[edit]

Main article: Soil microbiology

Microbes can make nutrients and minerals in the soil available to plants, produce hormones that spur growth, stimulate the plant immune system and trigger or dampen stress responses. In general a more diverse set of soil microbes results in fewer plant diseases and higher yield.[108]

Human health[edit]

Human gut flora[edit]

Further information: Human microbiota and Human Microbiome Project

Microorganisms can form an endosymbiotic relationship with other, larger organisms. For example, microbial symbiosis plays a crucial role in the immune system. The microorganisms that make up the gut flora in the gastrointestinal tract contribute to gut immunity, synthesize vitamins such as folic acid and biotin, and ferment complex indigestible carbohydrates.[109] Some microorganisms that are seen to be beneficial to health are termed probiotics and are available as dietary supplements, or food additives.[110]

Disease[edit]

Main articles: Pathogen and Germ theory of disease
Further information: Medical microbiology and Parasite
The eukaryotic parasite Plasmodium falciparum (spiky blue shapes), a causative agent of malaria, in human blood

Microorganisms are the causative agents (pathogens) in many infectious diseases. The organisms involved include pathogenic bacteria, causing diseases such as plague, tuberculosis and anthrax; protozoan parasites, causing diseases such as malaria, sleeping sickness, dysentery and toxoplasmosis; and also fungi causing diseases such as ringworm, candidiasis or histoplasmosis. However, other diseases such as influenza, yellow fever or AIDS are caused by pathogenic viruses, which are not usually classified as living organisms and are not, therefore, microorganisms by the strict definition. No clear examples of archaean pathogens are known,[111] although a relationship has been proposed between the presence of some archaean methanogens and human periodontal disease.[112] Numerous microbial pathogens are capable of sexual processes that appear to facilitate their survival in their infected host.[113]

Hygiene[edit]

Main articles: Hygiene and Food microbiology

Hygiene is a set of practices to avoid infection or food spoilage by eliminating microorganisms from the surroundings. As microorganisms, in particular bacteria, are found virtually everywhere, harmful microorganisms may be reduced to acceptable levels rather than actually eliminated. In food preparation, microorganisms are reduced by preservation methods such as cooking, cleanliness of utensils, short storage periods, or by low temperatures. If complete sterility is needed, as with surgical equipment, an autoclave is used to kill microorganisms with heat and pressure.[114][115]

In fiction[edit]

  • Osmosis Jones, a 2001 film, and its show Ozzy & Drix, set in a stylized version of the human body, featured anthropomorphic microorganisms.
  • War of the Worlds (2005 film), when Alien lifeforms attempt to conquer earth, they are ultimately defeated by a common Microbe to which Humans are immune.

See also[edit]

  • Catalogue of Life
  • Impedance microbiology
  • Microbial biogeography
  • Microbial intelligence
  • Microbiological culture
  • Microbivory, an eating behavior of some animals feeding on living microbes
  • Nanobacterium
  • Nylon-eating bacteria
  • Petri dish
  • Staining

Notes[edit]

  1. ^ The word microorganism (/ˌmaɪkroʊˈɔːrɡənɪzəm/) uses combining forms of micro- (from the Greek: μικρός, mikros, "small") and organism from the Greek: ὀργανισμός, organismós, "organism"). It is usually written as a single word but is sometimes hyphenated (micro-organism), especially in older texts. The informal synonym microbe (/ˈmaɪkroʊb/) comes from μικρός, mikrós, "small" and βίος, bíos, "life".

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From Wikipedia, the free encyclopedia
Infectious agent that replicates in cells
This article is about the type of pathogen. For the type of malware, see Computer virus. For other uses, see Virus (disambiguation).

For a more accessible and less technical introduction to this topic, see Introduction to viruses.

Virus
"Severe acute respiratory syndrome coronavirus 2"
SARS-CoV-2, a member of the subfamily Coronavirinae
Virus classification Edit this classification
(unranked): Virus
Realms
  • Adnaviria
  • Duplodnaviria
  • Monodnaviria
  • Riboviria
  • Ribozyviria
  • Varidnaviria

A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism.[1] Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea.[2][3] Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity.[4][5] Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898,[6] more than 11,000 of the millions of virus species have been described in detail.[7][8] The study of viruses is known as virology, a subspeciality of microbiology.

When infected, a host cell is often forced to rapidly produce thousands of copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent viral particles, or virions, consisting of (i) genetic material, i.e., long molecules of DNA or RNA that encode the structure of the proteins by which the virus acts; (ii) a protein coat, the capsid, which surrounds and protects the genetic material; and in some cases (iii) an outside envelope of lipids. The shapes of these virus particles range from simple helical and icosahedral forms to more complex structures. Most virus species have virions too small to be seen with an optical microscope and are one-hundredth the size of most bacteria.

The origins of viruses in the evolutionary history of life are unclear: some may have evolved from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity in a way analogous to sexual reproduction.[9] Viruses are considered by some biologists to be a life form, because they carry genetic material, reproduce, and evolve through natural selection, although they lack the key characteristics, such as cell structure, that are generally considered necessary criteria for defining life. Because they possess some but not all such qualities, viruses have been described as "organisms at the edge of life"[10] and as replicators.[11]

Viruses spread in many ways. One transmission pathway is through disease-bearing organisms known as vectors: for example, viruses are often transmitted from plant to plant by insects that feed on plant sap, such as aphids; and viruses in animals can be carried by blood-sucking insects. Many viruses spread in the air by coughing and sneezing, including influenza viruses, SARS-CoV-2, chickenpox, smallpox, and measles. Norovirus and rotavirus, common causes of viral gastroenteritis, are transmitted by the faecal–oral route, passed by hand-to-mouth contact or in food or water. The infectious dose of norovirus required to produce infection in humans is fewer than 100 particles.[12] HIV is one of several viruses transmitted through sexual contact and by exposure to infected blood. The variety of host cells that a virus can infect is called its host range: this is narrow for viruses specialized to infect only a few species, or broad for viruses capable of infecting many.[13]

Viral infections in animals provoke an immune response that usually eliminates the infecting virus. Immune responses can also be produced by vaccines, which confer an artificially acquired immunity to the specific viral infection. Some viruses, including those that cause HIV/AIDS, HPV infection, and viral hepatitis, evade these immune responses and result in chronic infections. Several classes of antiviral drugs have been developed.

Etymology

See also: Plural form of words ending in -us

The word is from the Latin neuter vīrus referring to poison and other noxious liquids, from the same Indo-European base as Sanskrit viṣa, Avestan vīša, and ancient Greek ἰός (all meaning 'poison'), first attested in English in 1398 in John Trevisa's translation of Bartholomeus Anglicus's De Proprietatibus Rerum.[14][15] Virulent, from Latin virulentus ('poisonous'), dates to c. 1400.[16][17] A meaning of 'agent that causes infectious disease' is first recorded in 1728,[15] long before the discovery of viruses by Dmitri Ivanovsky in 1892. The English plural is viruses (sometimes also vira),[18] whereas the Latin word is a mass noun, which has no classically attested plural (vīra is used in Neo-Latin[19]). The adjective viral dates to 1948.[20] The term virion (plural virions), which dates from 1959,[21] is also used to refer to a single viral particle that is released from the cell and is capable of infecting other cells of the same type.[22]

Origins

See also: Viral evolution

Viruses are found wherever there is life and have probably existed since living cells first evolved.[23] The origin of viruses is unclear because they do not form fossils, so molecular techniques are used to infer how they arose.[24] In addition, viral genetic material occasionally integrates into the germline of the host organisms, by which they can be passed on vertically to the offspring of the host for many generations. This provides an invaluable source of information for paleovirologists to trace back ancient viruses that existed as far back as millions of years ago.

There are three main hypotheses that aim to explain the origins of viruses:[25]

Regressive hypothesis
Viruses may have once been small cells that parasitised larger cells. Over time, genes not required by their parasitism were lost. The bacteria rickettsia and chlamydia are living cells that, like viruses, can reproduce only inside host cells. They lend support to this hypothesis, as their dependence on parasitism is likely to have caused the loss of genes that enabled them to survive outside a cell. This is also called the 'degeneracy hypothesis',[26][27] or 'reduction hypothesis'.[28]
Cellular origin hypothesis
Some viruses may have evolved from bits of DNA or RNA that "escaped" from the genes of a larger organism. The escaped DNA could have come from plasmids (pieces of naked DNA that can move between cells) or transposons (molecules of DNA that replicate and move around to different positions within the genes of the cell).[29] Once called jumping genes, transposons are examples of mobile genetic elements and could be the origin of some viruses. They were discovered in maize by Barbara McClintock in 1950.[30] This is sometimes called the 'vagrancy hypothesis',[26][31] or the 'escape hypothesis'.[28]
Co-evolution hypothesis
This is also called the 'virus-first hypothesis'[28] and proposes that viruses may have evolved from complex molecules of protein and nucleic acid at the same time that cells first appeared on Earth and would have been dependent on cellular life for billions of years. Viroids are molecules of RNA that are not classified as viruses because they lack a protein coat. They have characteristics that are common to several viruses and are often called subviral agents.[32] Viroids are important pathogens of plants.[33] They do not code for proteins but interact with the host cell and use the host machinery for their replication.[34] The hepatitis delta virus of humans has an RNA genome similar to viroids but has a protein coat derived from hepatitis B virus and cannot produce one of its own. It is, therefore, a defective virus. Although hepatitis delta virus genome may replicate independently once inside a host cell, it requires the help of hepatitis B virus to provide a protein coat so that it can be transmitted to new cells.[35] In similar manner, the sputnik virophage is dependent on mimivirus, which infects the protozoan Acanthamoeba castellanii.[36] These viruses, which are dependent on the presence of other virus species in the host cell, are called 'satellites' and may represent evolutionary intermediates of viroids and viruses.[37][38]

In the past, there were problems with all of these hypotheses: the regressive hypothesis did not explain why even the smallest of cellular parasites do not resemble viruses in any way. The escape hypothesis did not explain the complex capsids and other structures on virus particles. The virus-first hypothesis contravened the definition of viruses in that they require host cells.[28] Viruses are now recognised as ancient and as having origins that pre-date the divergence of life into the three domains.[39] This discovery has led modern virologists to reconsider and re-evaluate these three classical hypotheses.[39]

The evidence for an ancestral world of RNA cells[40] and computer analysis of viral and host DNA sequences are giving a better understanding of the evolutionary relationships between different viruses and may help identify the ancestors of modern viruses. To date, such analyses have not proved which of these hypotheses is correct.[40] It seems unlikely that all currently known viruses have a common ancestor, and viruses have probably arisen numerous times in the past by one or more mechanisms.[41]

Microbiology

Life properties

Scientific opinions differ on whether viruses are a form of life or organic structures that interact with living organisms.[11] They have been described as "organisms at the edge of life",[10] since they resemble organisms in that they possess genes, evolve by natural selection,[42] and reproduce by creating multiple copies of themselves through self-assembly. Although they have genes, they do not have a cellular structure, which is often seen as the basic unit of life. Viruses do not have their own metabolism and require a host cell to make new products. They therefore cannot naturally reproduce outside a host cell[43]—although some bacteria such as rickettsia and chlamydia are considered living organisms despite the same limitation.[44][45] Accepted forms of life use cell division to reproduce, whereas viruses spontaneously assemble within cells. They differ from autonomous growth of crystals as they inherit genetic mutations while being subject to natural selection. Virus self-assembly within host cells has implications for the study of the origin of life, as it lends further credence to the hypothesis that life could have started as self-assembling organic molecules.[2]

Structure

Virions of some of the most common human viruses with their relative size. The nucleic acids are not to scale.
Diagram of how a virus capsid can be constructed using multiple copies of just two protein molecules
Structure of tobacco mosaic virus: RNA coiled in a helix of repeating protein sub-units
Structure of icosahedral adenovirus. Electron micrograph with an illustration to show shape
Structure of chickenpox virus. They have a lipid envelope
Structure of an icosahedral cowpea mosaic virus
Bacteriophage Escherichia virus MS2 capsid. This spherical virus also has icosahedral symmetry.

Viruses display a wide diversity of sizes and shapes, called 'morphologies'. In general, viruses are much smaller than bacteria and more than a thousand bacteriophage viruses would fit inside an Escherichia coli bacterium's cell.[46] Many viruses that have been studied are spherical and have a diameter between 20 and 300 nanometres. Some filoviruses, which are filaments, have a total length of up to 1400 nm; their diameters are only about 80 nm.[47] Most viruses cannot be seen with an optical microscope, so scanning and transmission electron microscopes are used to visualise them.[48] To increase the contrast between viruses and the background, electron-dense "stains" are used. These are solutions of salts of heavy metals, such as tungsten, that scatter the electrons from regions covered with the stain. When virions are coated with stain (positive staining), fine detail is obscured. Negative staining overcomes this problem by staining the background only.[49]

A complete virus particle, known as a virion, consists of nucleic acid surrounded by a protective coat of protein called a capsid. These are formed from protein subunits called capsomeres.[50] Viruses can have a lipid "envelope" derived from the host cell membrane. The capsid is made from proteins encoded by the viral genome and its shape serves as the basis for morphological distinction.[51][52] Virally-coded protein subunits will self-assemble to form a capsid, in general requiring the presence of the virus genome. Complex viruses code for proteins that assist in the construction of their capsid. Proteins associated with nucleic acid are known as nucleoproteins, and the association of viral capsid proteins with viral nucleic acid is called a nucleocapsid. The capsid and entire virus structure can be mechanically (physically) probed through atomic force microscopy.[53][54] In general, there are five main morphological virus types:

Helical
These viruses are composed of a single type of capsomere stacked around a central axis to form a helical structure, which may have a central cavity, or tube. This arrangement results in virions which can be short and highly rigid rods, or long and very flexible filaments. The genetic material (typically single-stranded RNA, but single-stranded DNA in some cases) is bound into the protein helix by interactions between the negatively charged nucleic acid and positive charges on the protein. Overall, the length of a helical capsid is related to the length of the nucleic acid contained within it, and the diameter is dependent on the size and arrangement of capsomeres. The well-studied tobacco mosaic virus[55] and inovirus[56] are examples of helical viruses.
Icosahedral
Most animal viruses are icosahedral or near-spherical with chiral icosahedral symmetry. A regular icosahedron is the optimum way of forming a closed shell from identical subunits. The minimum number of capsomeres required for each triangular face is 3, which gives 60 for the icosahedron. Many viruses, such as rotavirus, have more than 60 capsomers and appear spherical but they retain this symmetry. To achieve this, the capsomeres at the apices are surrounded by five other capsomeres and are called pentons. Capsomeres on the triangular faces are surrounded by six others and are called hexons.[57] Hexons are in essence flat and pentons, which form the 12 vertices, are curved. The same protein may act as the subunit of both the pentamers and hexamers or they may be composed of different proteins.[58]
Prolate
This is an icosahedron elongated along the fivefold axis and is a common arrangement of the heads of bacteriophages. This structure is composed of a cylinder with a cap at either end.[59]
Enveloped
Some species of virus envelop themselves in a modified form of one of the cell membranes, either the outer membrane surrounding an infected host cell or internal membranes such as a nuclear membrane or endoplasmic reticulum, thus gaining an outer lipid bilayer known as a viral envelope. This membrane is studded with proteins coded for by the viral genome and host genome; the lipid membrane itself and any carbohydrates present originate entirely from the host. Influenza virus, HIV (which causes AIDS), and severe acute respiratory syndrome coronavirus 2 (which causes COVID-19)[60] use this strategy. Most enveloped viruses are dependent on the envelope for their infectivity.[61]
Complex
These viruses possess a capsid that is neither purely helical nor purely icosahedral, and that may possess extra structures such as protein tails or a complex outer wall. Some bacteriophages, such as Enterobacteria phage T4, have a complex structure consisting of an icosahedral head bound to a helical tail, which may have a hexagonal base plate with protruding protein tail fibres. This tail structure acts like a molecular syringe, attaching to the bacterial host and then injecting the viral genome into the cell.[62]

The poxviruses are large, complex viruses that have an unusual morphology. The viral genome is associated with proteins within a central disc structure known as a nucleoid. The nucleoid is surrounded by a membrane and two lateral bodies of unknown function. The virus has an outer envelope with a thick layer of protein studded over its surface. The whole virion is slightly pleomorphic, ranging from ovoid to brick-shaped.[63]

Giant viruses

Main article: Giant virus

Mimivirus is one of the largest characterised viruses, with a capsid diameter of 400 nm. Protein filaments measuring 100 nm project from the surface. The capsid appears hexagonal under an electron microscope, therefore the capsid is probably icosahedral.[64] In 2011, researchers discovered the largest then known virus in samples of water collected from the ocean floor off the coast of Las Cruces, Chile. Provisionally named Megavirus chilensis, it can be seen with a basic optical microscope.[65] In 2013, the Pandoravirus genus was discovered in Chile and Australia, and has genomes about twice as large as Megavirus and Mimivirus.[66] All giant viruses have dsDNA genomes and they are classified into several families: Mimiviridae, Pithoviridae, Pandoraviridae, Phycodnaviridae, and the Mollivirus genus.[67]

Some viruses that infect Archaea have complex structures unrelated to any other form of virus, with a wide variety of unusual shapes, ranging from spindle-shaped structures to viruses that resemble hooked rods, teardrops or even bottles. Other archaeal viruses resemble the tailed bacteriophages, and can have multiple tail structures.[68]

Genome

Genomic diversity among viruses
Property Parameters
Nucleic acid
  • DNA
  • RNA
  • Both DNA and RNA (at different stages in the life cycle)
Shape
  • Linear
  • Circular
  • Segmented
Strandedness
  • Single-stranded (ss)
  • Double-stranded (ds)
  • Double-stranded with regions of single-strandedness
Sense
  • Positive sense (+)
  • Negative sense (−)
  • Ambisense (+/−)

An enormous variety of genomic structures can be seen among viral species; as a group, they contain more structural genomic diversity than plants, animals, archaea, or bacteria. There are millions of different types of viruses,[8] although fewer than 7,000 types have been described in detail.[69] As of January 2021, the NCBI Virus genome database has more than 193,000 complete genome sequences,[70] but there are doubtlessly many more to be discovered.[71][72]

A virus has either a DNA or an RNA genome and is called a DNA virus or an RNA virus, respectively. The vast majority of viruses have RNA genomes. Plant viruses tend to have single-stranded RNA genomes and bacteriophages tend to have double-stranded DNA genomes.[73]

Viral genomes are circular, as in the polyomaviruses, or linear, as in the adenoviruses. The type of nucleic acid is irrelevant to the shape of the genome. Among RNA viruses and certain DNA viruses, the genome is often divided into separate parts, in which case it is called segmented. For RNA viruses, each segment often codes for only one protein and they are usually found together in one capsid. All segments are not required to be in the same virion for the virus to be infectious, as demonstrated by brome mosaic virus and several other plant viruses.[47]

A viral genome, irrespective of nucleic acid type, is almost always either single-stranded (ss) or double-stranded (ds). Single-stranded genomes consist of an unpaired nucleic acid, analogous to one-half of a ladder split down the middle. Double-stranded genomes consist of two complementary paired nucleic acids, analogous to a ladder. The virus particles of some virus families, such as those belonging to the Hepadnaviridae, contain a genome that is partially double-stranded and partially single-stranded.[73]

For most viruses with RNA genomes and some with single-stranded DNA (ssDNA) genomes, the single strands are said to be either positive-sense (called the 'plus-strand') or negative-sense (called the 'minus-strand'), depending on if they are complementary to the viral messenger RNA (mRNA). Positive-sense viral RNA is in the same sense as viral mRNA and thus at least a part of it can be immediately translated by the host cell. Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA-dependent RNA polymerase before translation. DNA nomenclature for viruses with genomic ssDNA is similar to RNA nomenclature, in that positive-strand viral ssDNA is identical in sequence to the viral mRNA and is thus a coding strand, while negative-sense viral ssDNA is complementary to the viral mRNA and is thus a template strand.[73] Several types of ssDNA and ssRNA viruses have genomes that are ambisense in that transcription can occur off both strands in a double-stranded replicative intermediate. Examples include geminiviruses, which are ssDNA plant viruses and arenaviruses, which are ssRNA viruses of animals.[74]

Genome size

Genome size varies greatly between species. The smallest—the ssDNA circoviruses, family Circoviridae—code for only two proteins and have a genome size of only two kilobases;[75] the largest—the pandoraviruses—have genome sizes of around two megabases which code for about 2500 proteins.[66] Virus genes rarely have introns and often are arranged in the genome so that they overlap.[76]

In general, RNA viruses have smaller genome sizes than DNA viruses because of a higher error-rate when replicating, and have a maximum upper size limit.[24] Beyond this, errors when replicating render the virus useless or uncompetitive. To compensate, RNA viruses often have segmented genomes—the genome is split into smaller molecules—thus reducing the chance that an error in a single-component genome will incapacitate the entire genome. In contrast, DNA viruses generally have larger genomes because of the high fidelity of their replication enzymes.[77] Single-strand DNA viruses are an exception to this rule, as mutation rates for these genomes can approach the extreme of the ssRNA virus case.[78]

Genetic mutation and recombination

A cartoon showing how viral genes can be shuffled to form new viruses
Antigenic shift, or reassortment, can result in novel and highly pathogenic strains of human flu

Viruses undergo genetic change by several mechanisms. These include a process called antigenic drift where individual bases in the DNA or RNA mutate to other bases. Most of these point mutations are "silent"—they do not change the protein that the gene encodes—but others can confer evolutionary advantages such as resistance to antiviral drugs.[79][80] Antigenic shift occurs when there is a major change in the genome of the virus. This can be a result of recombination or reassortment. When this happens with influenza viruses, pandemics might result.[81] RNA viruses often exist as quasispecies or swarms of viruses of the same species but with slightly different genome nucleoside sequences. Such quasispecies are a prime target for natural selection.[82]

Segmented genomes confer evolutionary advantages; different strains of a virus with a segmented genome can shuffle and combine genes and produce progeny viruses (or offspring) that have unique characteristics. This is called reassortment or 'viral sex'.[83]

Genetic recombination is a process by which a strand of DNA (or RNA) is broken and then joined to the end of a different DNA (or RNA) molecule. This can occur when viruses infect cells simultaneously and studies of viral evolution have shown that recombination has been rampant in the species studied.[84] Recombination is common to both RNA and DNA viruses.[85][86]

Coronaviruses have a single-strand positive-sense RNA genome. Replication of the genome is catalyzed by an RNA-dependent RNA polymerase. The mechanism of recombination used by coronaviruses likely involves template switching by the polymerase during genome replication.[87] This process appears to be an adaptation for coping with genome damage.[88]

Replication cycle

A typical virus replication cycle
Some bacteriophages inject their genomes into bacterial cells (not to scale)

Viral populations do not grow through cell division, because they are acellular. Instead, they use the machinery and metabolism of a host cell to produce multiple copies of themselves, and they assemble in the cell.[89] When infected, the host cell is forced to rapidly produce thousands of copies of the original virus.[90]

Their life cycle differs greatly between species, but there are six basic stages in their life cycle:[91]

Attachment is a specific binding between viral capsid proteins and specific receptors on the host cellular surface. This specificity determines the host range and type of host cell of a virus. For example, HIV infects a limited range of human leucocytes. This is because its surface protein, gp120, specifically interacts with the CD4 molecule—a chemokine receptor—which is most commonly found on the surface of CD4+ T-Cells. This mechanism has evolved to favour those viruses that infect only cells in which they are capable of replication. Attachment to the receptor can induce the viral envelope protein to undergo changes that result in the fusion of viral and cellular membranes, or changes of non-enveloped virus surface proteins that allow the virus to enter.[92]

Penetration or viral entry follows attachment: Virions enter the host cell through receptor-mediated endocytosis or membrane fusion. The infection of plant and fungal cells is different from that of animal cells. Plants have a rigid cell wall made of cellulose, and fungi one of chitin, so most viruses can get inside these cells only after trauma to the cell wall.[93] Nearly all plant viruses (such as tobacco mosaic virus) can also move directly from cell to cell, in the form of single-stranded nucleoprotein complexes, through pores called plasmodesmata.[94] Bacteria, like plants, have strong cell walls that a virus must breach to infect the cell. Given that bacterial cell walls are much thinner than plant cell walls due to their much smaller size, some viruses have evolved mechanisms that inject their genome into the bacterial cell across the cell wall, while the viral capsid remains outside.[95]

Uncoating is a process in which the viral capsid is removed: This may be by degradation by viral enzymes or host enzymes or by simple dissociation; the end-result is the releasing of the viral genomic nucleic acid.[96]

Replication of viruses involves primarily multiplication of the genome. Replication involves the synthesis of viral messenger RNA (mRNA) from "early" genes (with exceptions for positive-sense RNA viruses), viral protein synthesis, possible assembly of viral proteins, then viral genome replication mediated by early or regulatory protein expression. This may be followed, for complex viruses with larger genomes, by one or more further rounds of mRNA synthesis: "late" gene expression is, in general, of structural or virion proteins.[97]

Assembly – Following the structure-mediated self-assembly of the virus particles, some modification of the proteins often occurs. In viruses such as HIV, this modification (sometimes called maturation) occurs after the virus has been released from the host cell.[98]

Release – Viruses can be released from the host cell by lysis, a process that kills the cell by bursting its membrane and cell wall if present: this is a feature of many bacterial and some animal viruses. Some viruses undergo a lysogenic cycle where the viral genome is incorporated by genetic recombination into a specific place in the host's chromosome. The viral genome is then known as a "provirus" or, in the case of bacteriophages a "prophage".[99] Whenever the host divides, the viral genome is also replicated. The viral genome is mostly silent within the host. At some point, the provirus or prophage may give rise to the active virus, which may lyse the host cells.[100] Enveloped viruses (e.g., HIV) typically are released from the host cell by budding. During this process, the virus acquires its envelope, which is a modified piece of the host's plasma or other, internal membrane.[101]

Genome replication

The genetic material within virus particles, and the method by which the material is replicated, varies considerably between different types of viruses.

DNA viruses
The genome replication of most DNA viruses takes place in the cell's nucleus. If the cell has the appropriate receptor on its surface, these viruses enter the cell either by direct fusion with the cell membrane (e.g., herpesviruses) or—more usually—by receptor-mediated endocytosis. Most DNA viruses are entirely dependent on the host cell's DNA and RNA synthesising machinery and RNA processing machinery. Viruses with larger genomes may encode much of this machinery themselves. In eukaryotes, the viral genome must cross the cell's nuclear membrane to access this machinery, while in bacteria it need only enter the cell.[102]
RNA viruses
Replication of RNA viruses usually takes place in the cytoplasm. RNA viruses can be placed into four different groups depending on their modes of replication. The polarity (whether or not it can be used directly by ribosomes to make proteins) of single-stranded RNA viruses largely determines the replicative mechanism; the other major criterion is whether the genetic material is single-stranded or double-stranded. All RNA viruses use their own RNA replicase enzymes to create copies of their genomes.[103]
Reverse transcribing viruses
Reverse transcribing viruses have ssRNA (Retroviridae, Metaviridae, Pseudoviridae) or dsDNA (Caulimoviridae, and Hepadnaviridae) in their particles. Reverse transcribing viruses with RNA genomes (retroviruses) use a DNA intermediate to replicate, whereas those with DNA genomes (pararetroviruses) use an RNA intermediate during genome replication. Both types use a reverse transcriptase, or RNA-dependent DNA polymerase enzyme, to carry out the nucleic acid conversion. Retroviruses integrate the DNA produced by reverse transcription into the host genome as a provirus as a part of the replication process; pararetroviruses do not, although integrated genome copies of especially plant pararetroviruses can give rise to infectious virus.[104] They are susceptible to antiviral drugs that inhibit the reverse transcriptase enzyme, e.g. zidovudine and lamivudine. An example of the first type is HIV, which is a retrovirus. Examples of the second type are the Hepadnaviridae, which includes Hepatitis B virus.[105]

Cytopathic effects on the host cell

The range of structural and biochemical effects that viruses have on the host cell is extensive.[106] These are called 'cytopathic effects'.[107] Most virus infections eventually result in the death of the host cell. The causes of death include cell lysis, alterations to the cell's surface membrane and apoptosis.[108] Often cell death is caused by cessation of its normal activities because of suppression by virus-specific proteins, not all of which are components of the virus particle.[109] The distinction between cytopathic and harmless is gradual. Some viruses, such as Epstein–Barr virus, can cause cells to proliferate without causing malignancy,[110] while others, such as papillomaviruses, are established causes of cancer.[111]

Dormant and latent infections

Some viruses cause no apparent changes to the infected cell. Cells in which the virus is latent and inactive show few signs of infection and often function normally.[112] This causes persistent infections and the virus is often dormant for many months or years. This is often the case with herpes viruses.[113][114]

Host range

Viruses are by far the most abundant biological entities on Earth and they outnumber all the others put together.[115] They infect all types of cellular life including animals, plants, bacteria and fungi.[69] Different types of viruses can infect only a limited range of hosts and many are species-specific. Some, such as smallpox virus for example, can infect only one species—in this case humans,[116] and are said to have a narrow host range. Other viruses, such as rabies virus, can infect different species of mammals and are said to have a broad range.[117] The viruses that infect plants are harmless to animals, and most viruses that infect other animals are harmless to humans.[118] The host range of some bacteriophages is limited to a single strain of bacteria and they can be used to trace the source of outbreaks of infections by a method called phage typing.[119] The complete set of viruses in an organism or habitat is called the virome; for example, all human viruses constitute the human virome.[120]

Novel viruses

A novel virus is one that has not previously been recorded. It can be a virus that is isolated from its natural reservoir or isolated as the result of spread to an animal or human host where the virus had not been identified before. It can be an emergent virus, one that represents a new virus, but it can also be an extant virus that has not been previously identified.[121] The SARS-CoV-2 coronavirus that caused the COVID-19 pandemic is an example of a novel virus.[122]

Classification

Main article: Virus classification

Classification seeks to describe the diversity of viruses by naming and grouping them on the basis of similarities. In 1962, André Lwoff, Robert Horne, and Paul Tournier were the first to develop a means of virus classification, based on the Linnaean hierarchical system.[123] This system based classification on phylum, class, order, family, genus, and species. Viruses were grouped according to their shared properties (not those of their hosts) and the type of nucleic acid forming their genomes.[124] In 1966, the International Committee on Taxonomy of Viruses (ICTV) was formed. The system proposed by Lwoff, Horne and Tournier was initially not accepted by the ICTV because the small genome size of viruses and their high rate of mutation made it difficult to determine their ancestry beyond order. As such, the Baltimore classification system has come to be used to supplement the more traditional hierarchy.[125] Starting in 2018, the ICTV began to acknowledge deeper evolutionary relationships between viruses that have been discovered over time and adopted a 15-rank classification system ranging from realm to species.[126] Additionally, some species within the same genus are grouped into a genogroup.[127][128]

ICTV classification

The ICTV developed the current classification system and wrote guidelines that put a greater weight on certain virus properties to maintain family uniformity. A unified taxonomy (a universal system for classifying viruses) has been established.[129] Only a small part of the total diversity of viruses has been studied.[130] As of 2022, 6 realms, 10 kingdoms, 17 phyla, 2 subphyla, 40 classes, 72 orders, 8 suborders, 264 families, 182 subfamilies, 2,818 genera, 84 subgenera, and 11,273 species of viruses have been defined by the ICTV.[7]

The general taxonomic structure of taxon ranges and the suffixes used in taxonomic names are shown hereafter. As of 2022, the ranks of subrealm, subkingdom, and subclass are unused, whereas all other ranks are in use.[7]

Realm (-viria)
Subrealm (-vira)
Kingdom (-virae)
Subkingdom (-virites)
Phylum (-viricota)
Subphylum (-viricotina)
Class (-viricetes)
Subclass (-viricetidae)
Order (-virales)
Suborder (-virineae)
Family (-viridae)
Subfamily (-virinae)
Genus (-virus)
Subgenus (-virus)
Species

Baltimore classification

Main article: Baltimore classification
A diagram showing how the Baltimore Classification is based on a virus's DNA or RNA and method of mRNA synthesis
The Baltimore Classification of viruses is based on the method of viral mRNA synthesis

The Nobel Prize-winning biologist David Baltimore devised the Baltimore classification system.[131][132] The ICTV classification system is used in conjunction with the Baltimore classification system in modern virus classification.[133][134][135]

The Baltimore classification of viruses is based on the mechanism of mRNA production. Viruses must generate mRNAs from their genomes to produce proteins and replicate themselves, but different mechanisms are used to achieve this in each virus family. Viral genomes may be single-stranded (ss) or double-stranded (ds), RNA or DNA, and may or may not use reverse transcriptase (RT). In addition, ssRNA viruses may be either sense (+) or antisense (−). This classification places viruses into seven groups:

  • I: dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses)
  • II: ssDNA viruses (+ strand or "sense") DNA (e.g. Parvoviruses)
  • III: dsRNA viruses (e.g. Reoviruses)
  • IV:(+)ssRNA viruses (+ strand or sense) RNA (e.g. Coronaviruses, Picornaviruses, Togaviruses)
  • V: (−)ssRNA viruses (− strand or antisense) RNA (e.g. Orthomyxoviruses, Rhabdoviruses)
  • VI: ssRNA-RT viruses (+ strand or sense) RNA with DNA intermediate in life-cycle (e.g. Retroviruses)
  • VII: dsDNA-RT viruses DNA with RNA intermediate in life-cycle (e.g. Hepadnaviruses)


Role in human disease

See also: Viral disease
A photograph of the upper body of a man labelled with the names of viruses that infect the different parts
Overview of the main types of viral infection and the most notable species involved[136]

Examples of common human diseases caused by viruses include the common cold, influenza, chickenpox, and cold sores. Many serious diseases such as rabies, Ebola virus disease, AIDS (HIV), avian influenza, and SARS are caused by viruses. The relative ability of viruses to cause disease is described in terms of virulence. Other diseases are under investigation to discover if they have a virus as the causative agent, such as the possible connection between human herpesvirus 6 (HHV6) and neurological diseases such as multiple sclerosis and chronic fatigue syndrome.[137] There is controversy over whether the bornavirus, previously thought to cause neurological diseases in horses, could be responsible for psychiatric illnesses in humans.[138]

Viruses have different mechanisms by which they produce disease in an organism, which depends largely on the viral species. Mechanisms at the cellular level primarily include cell lysis, the breaking open and subsequent death of the cell. In multicellular organisms, if enough cells die, the whole organism will start to suffer the effects. Although viruses cause disruption of healthy homeostasis, resulting in disease, they may exist relatively harmlessly within an organism. An example would include the ability of the herpes simplex virus, which causes cold sores, to remain in a dormant state within the human body. This is called latency[139] and is a characteristic of the herpes viruses, including Epstein–Barr virus, which causes glandular fever, and varicella zoster virus, which causes chickenpox and shingles. Most people have been infected with at least one of these types of herpes virus.[140] These latent viruses might sometimes be beneficial, as the presence of the virus can increase immunity against bacterial pathogens, such as Yersinia pestis.[141]

Some viruses can cause lifelong or chronic infections, where the viruses continue to replicate in the body despite the host's defence mechanisms.[142] This is common in hepatitis B virus and hepatitis C virus infections. People chronically infected are known as carriers, as they serve as reservoirs of infectious virus.[143] In populations with a high proportion of carriers, the disease is said to be endemic.[144]

Epidemiology

Viral epidemiology is the branch of medical science that deals with the transmission and control of virus infections in humans. Transmission of viruses can be vertical, which means from mother to child, or horizontal, which means from person to person. Examples of vertical transmission include hepatitis B virus and HIV, where the baby is born already infected with the virus.[145] Another, more rare, example is the varicella zoster virus, which, although causing relatively mild infections in children and adults, can be fatal to the foetus and newborn baby.[146]

Horizontal transmission is the most common mechanism of spread of viruses in populations.[147] Horizontal transmission can occur when body fluids are exchanged during sexual activity, by exchange of saliva or when contaminated food or water is ingested. It can also occur when aerosols containing viruses are inhaled or by insect vectors such as when infected mosquitoes penetrate the skin of a host.[147] Most types of viruses are restricted to just one or two of these mechanisms and they are referred to as "respiratory viruses" or "enteric viruses" and so forth. The rate or speed of transmission of viral infections depends on factors that include population density, the number of susceptible individuals, (i.e., those not immune),[148] the quality of healthcare and the weather.[149]

Epidemiology is used to break the chain of infection in populations during outbreaks of viral diseases.[150] Control measures are used that are based on knowledge of how the virus is transmitted. It is important to find the source, or sources, of the outbreak and to identify the virus. Once the virus has been identified, the chain of transmission can sometimes be broken by vaccines. When vaccines are not available, sanitation and disinfection can be effective. Often, infected people are isolated from the rest of the community, and those that have been exposed to the virus are placed in quarantine.[151] To control the outbreak of foot-and-mouth disease in cattle in Britain in 2001, thousands of cattle were slaughtered.[152] Most viral infections of humans and other animals have incubation periods during which the infection causes no signs or symptoms.[153] Incubation periods for viral diseases range from a few days to weeks, but are known for most infections.[154] Somewhat overlapping, but mainly following the incubation period, there is a period of communicability—a time when an infected individual or animal is contagious and can infect another person or animal.[154] This, too, is known for many viral infections, and knowledge of the length of both periods is important in the control of outbreaks.[155] When outbreaks cause an unusually high proportion of cases in a population, community, or region, they are called epidemics. If outbreaks spread worldwide, they are called pandemics.[156]

Epidemics and pandemics

See also: 1918 flu pandemic, AIDS, Ebola virus disease, and COVID-19 pandemic
Further information: List of epidemics
An electron micrograph of the virus that caused Spanish influenza
Transmission electron microscope image of a recreated 1918 influenza virus

A pandemic is a worldwide epidemic. The 1918 flu pandemic, which lasted until 1919, was a category 5 influenza pandemic caused by an unusually severe and deadly influenza A virus. The victims were often healthy young adults, in contrast to most influenza outbreaks, which predominantly affect juvenile, elderly, or otherwise-weakened patients.[157] Older estimates say it killed 40–50 million people,[158] while more recent research suggests that it may have killed as many as 100 million people, or 5% of the world's population in 1918.[159]

Although viral pandemics are rare events, HIV—which evolved from viruses found in monkeys and chimpanzees—has been pandemic since at least the 1980s.[160] During the 20th century there were four pandemics caused by influenza virus and those that occurred in 1918, 1957 and 1968 were severe.[161] Most researchers believe that HIV originated in sub-Saharan Africa during the 20th century;[162] it is now a pandemic, with an estimated 37.9 million people now living with the disease worldwide.[163] There were about 770,000 deaths from AIDS in 2018.[164] The Joint United Nations Programme on HIV/AIDS (UNAIDS) and the World Health Organization (WHO) estimate that AIDS has killed more than 25 million people since it was first recognised on 5 June 1981, making it one of the most destructive epidemics in recorded history.[165] In 2007 there were 2.7 million new HIV infections and 2 million HIV-related deaths.[166]

Ebola (top) and Marburg viruses (bottom)

Several highly lethal viral pathogens are members of the Filoviridae. Filoviruses are filament-like viruses that cause viral hemorrhagic fever, and include ebolaviruses and marburgviruses. Marburg virus, first discovered in 1967, attracted widespread press attention in April 2005 for an outbreak in Angola.[167] Ebola virus disease has also caused intermittent outbreaks with high mortality rates since 1976 when it was first identified. The worst and most recent one is the 2013–2016 West Africa epidemic.[168]

Except for smallpox, most pandemics are caused by newly evolved viruses. These "emergent" viruses are usually mutants of less harmful viruses that have circulated previously either in humans or other animals.[169]

Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) are caused by new types of coronaviruses. Other coronaviruses are known to cause mild infections in humans,[170] so the virulence and rapid spread of SARS infections—that by July 2003 had caused around 8,000 cases and 800 deaths—was unexpected and most countries were not prepared.[171]

A related coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2), thought to have originated in bats, emerged in Wuhan, China in November 2019 and spread rapidly around the world. Infections with the virus caused the COVID-19 pandemic that started in 2020.[122][172][173] Unprecedented restrictions in peacetime were placed on international travel,[174] and curfews were imposed in several major cities worldwide in response to the pandemic.[175]

Cancer

Further information: Oncovirus

Viruses are an established cause of cancer in humans and other species. Viral cancers occur only in a minority of infected persons (or animals). Cancer viruses come from a range of virus families, including both RNA and DNA viruses, and so there is no single type of "oncovirus" (an obsolete term originally used for acutely transforming retroviruses). The development of cancer is determined by a variety of factors such as host immunity[176] and mutations in the host.[177] Viruses accepted to cause human cancers include some genotypes of human papillomavirus, hepatitis B virus, hepatitis C virus, Epstein–Barr virus, Kaposi's sarcoma-associated herpesvirus and human T-lymphotropic virus. The most recently discovered human cancer virus is a polyomavirus (Merkel cell polyomavirus) that causes most cases of a rare form of skin cancer called Merkel cell carcinoma.[178] Hepatitis viruses can develop into a chronic viral infection that leads to liver cancer.[179][180] Infection by human T-lymphotropic virus can lead to tropical spastic paraparesis and adult T-cell leukaemia.[181] Human papillomaviruses are an established cause of cancers of cervix, skin, anus, and penis.[182] Within the Herpesviridae, Kaposi's sarcoma-associated herpesvirus causes Kaposi's sarcoma and body-cavity lymphoma, and Epstein–Barr virus causes Burkitt's lymphoma, Hodgkin's lymphoma, B lymphoproliferative disorder, and nasopharyngeal carcinoma.[183] Merkel cell polyomavirus closely related to SV40 and mouse polyomaviruses that have been used as animal models for cancer viruses for over 50 years.[184]

Host defence mechanisms

See also: Immune system

The body's first line of defence against viruses is the innate immune system. This comprises cells and other mechanisms that defend the host from infection in a non-specific manner. This means that the cells of the innate system recognise, and respond to, pathogens in a generic way, but, unlike the adaptive immune system, it does not confer long-lasting or protective immunity to the host.[185]

RNA interference is an important innate defence against viruses.[186] Many viruses have a replication strategy that involves double-stranded RNA (dsRNA). When such a virus infects a cell, it releases its RNA molecule or molecules, which immediately bind to a protein complex called a dicer that cuts the RNA into smaller pieces. A biochemical pathway—the RISC complex—is activated, which ensures cell survival by degrading the viral mRNA. Rotaviruses have evolved to avoid this defence mechanism by not uncoating fully inside the cell, and releasing newly produced mRNA through pores in the particle's inner capsid. Their genomic dsRNA remains protected inside the core of the virion.[187][188]

When the adaptive immune system of a vertebrate encounters a virus, it produces specific antibodies that bind to the virus and often render it non-infectious. This is called humoral immunity. Two types of antibodies are important. The first, called IgM, is highly effective at neutralising viruses but is produced by the cells of the immune system only for a few weeks. The second, called IgG, is produced indefinitely. The presence of IgM in the blood of the host is used to test for acute infection, whereas IgG indicates an infection sometime in the past.[189] IgG antibody is measured when tests for immunity are carried out.[190]

Antibodies can continue to be an effective defence mechanism even after viruses have managed to gain entry to the host cell. A protein that is in cells, called TRIM21, can attach to the antibodies on the surface of the virus particle. This primes the subsequent destruction of the virus by the enzymes of the cell's proteosome system.[191]

Two spherical rotavirus particles, one is coated with antibody which looks like many small birds, regularly spaced on the surface of the virus
Two rotaviruses: the one on the right is coated with antibodies that prevent its attachment to cells and infecting them.

A second defence of vertebrates against viruses is called cell-mediated immunity and involves immune cells known as T cells. The body's cells constantly display short fragments of their proteins on the cell's surface, and, if a T cell recognises a suspicious viral fragment there, the host cell is destroyed by 'killer T' cells and the virus-specific T-cells proliferate. Cells such as the macrophage are specialists at this antigen presentation.[192] The production of interferon is an important host defence mechanism. This is a hormone produced by the body when viruses are present. Its role in immunity is complex; it eventually stops the viruses from reproducing by killing the infected cell and its close neighbours.[193]

Not all virus infections produce a protective immune response in this way. HIV evades the immune system by constantly changing the amino acid sequence of the proteins on the surface of the virion. This is known as "escape mutation" as the viral epitopes escape recognition by the host immune response. These persistent viruses evade immune control by sequestration, blockade of antigen presentation, cytokine resistance, evasion of natural killer cell activities, escape from apoptosis, and antigenic shift.[194] Other viruses, called 'neurotropic viruses', are disseminated by neural spread where the immune system may be unable to reach them due to immune privilege.[195]

Prevention and treatment

Because viruses use vital metabolic pathways within host cells to replicate, they are difficult to eliminate without using drugs that cause toxic effects to host cells in general. The most effective medical approaches to viral diseases are vaccinations to provide immunity to infection, and antiviral drugs that selectively interfere with viral replication.

Vaccines

Further information: Vaccination

Vaccination is a cheap and effective way of preventing infections by viruses. Vaccines were used to prevent viral infections long before the discovery of the actual viruses. Their use has resulted in a dramatic decline in morbidity (illness) and mortality (death) associated with viral infections such as polio, measles, mumps and rubella.[196] Smallpox infections have been eradicated.[197] Vaccines are available to prevent over thirteen viral infections of humans,[198] and more are used to prevent viral infections of animals.[199] Vaccines can consist of live-attenuated or killed viruses, viral proteins (antigens), or RNA.[200][201] Live vaccines contain weakened forms of the virus, which do not cause the disease but, nonetheless, confer immunity. Such viruses are called attenuated. Live vaccines can be dangerous when given to people with a weak immunity (who are described as immunocompromised), because in these people, the weakened virus can cause the original disease.[202] Biotechnology and genetic engineering techniques are used to produce subunit vaccines. These vaccines use only the capsid proteins of the virus. Hepatitis B vaccine is an example of this type of vaccine.[203] Subunit vaccines are safe for immunocompromised patients because they cannot cause the disease.[204] The yellow fever virus vaccine, a live-attenuated strain called 17D, is probably the safest and most effective vaccine ever generated.[205]

Antiviral drugs

Further information: Antiviral drug
The structure of the DNA base guanosine and the antiviral drug acyclovir

Antiviral drugs are often nucleoside analogues (fake DNA building-blocks), which viruses mistakenly incorporate into their genomes during replication.[206] The life-cycle of the virus is then halted because the newly synthesised DNA is inactive. This is because these analogues lack the hydroxyl groups, which, along with phosphorus atoms, link together to form the strong "backbone" of the DNA molecule. This is called DNA chain termination.[207] Examples of nucleoside analogues are aciclovir for Herpes simplex virus infections and lamivudine for HIV and hepatitis B virus infections. Aciclovir is one of the oldest and most frequently prescribed antiviral drugs.[208] Other antiviral drugs in use target different stages of the viral life cycle. HIV is dependent on a proteolytic enzyme called the HIV-1 protease for it to become fully infectious. There is a large class of drugs called protease inhibitors that inactivate this enzyme.[209] There are around thirteen classes of antiviral drugs each targeting different viruses or stages of viral replication.[206]

Hepatitis C is caused by an RNA virus. In 80% of people infected, the disease is chronic, and without treatment, they are infected for the remainder of their lives. There are effective treatments that use direct-acting antivirals.[210] The treatment of chronic carriers of the hepatitis B virus has also been developed by using similar strategies that include lamivudine and other anti-viral drugs.[211]

Infection in other species

Viruses infect all cellular life and, although viruses occur universally, each cellular species has its own specific range that often infects only that species.[212] Some viruses, called satellites, can replicate only within cells that have already been infected by another virus.[36]

Animal viruses

Main articles: Animal virus and Veterinary virology

Viruses are important pathogens of livestock. Diseases such as foot-and-mouth disease and bluetongue are caused by viruses.[213] Companion animals such as cats, dogs, and horses, if not vaccinated, are susceptible to serious viral infections. Canine parvovirus is caused by a small DNA virus and infections are often fatal in pups.[214] Like all invertebrates, the honey bee is susceptible to many viral infections.[215] Most viruses co-exist harmlessly in their host and cause no signs or symptoms of disease.[6]

Plant viruses

Main article: Plant virus
Peppers infected by mild mottle virus

There are many types of plant viruses, but often they cause only a loss of yield, and it is not economically viable to try to control them. Plant viruses are often spread from plant to plant by organisms, known as vectors. These are usually insects, but some fungi, nematode worms, single-celled organisms, and parasitic plants are vectors.[216] When control of plant virus infections is considered economical, for perennial fruits, for example, efforts are concentrated on killing the vectors and removing alternate hosts such as weeds.[217] Plant viruses cannot infect humans and other animals because they can reproduce only in living plant cells.[218]

Originally from Peru, the potato has become a staple crop worldwide.[219] The potato virus Y causes disease in potatoes and related species including tomatoes and peppers. In the 1980s, this virus acquired economical importance when it proved difficult to control in seed potato crops. Transmitted by aphids, this virus can reduce crop yields by up to 80 per cent, causing significant losses to potato yields.[220]

Plants have elaborate and effective defence mechanisms against viruses. One of the most effective is the presence of so-called resistance (R) genes. Each R gene confers resistance to a particular virus by triggering localised areas of cell death around the infected cell, which can often be seen with the unaided eye as large spots. This stops the infection from spreading.[221] RNA interference is also an effective defence in plants.[222] When they are infected, plants often produce natural disinfectants that kill viruses, such as salicylic acid, nitric oxide, and reactive oxygen molecules.[223]

Plant virus particles or virus-like particles (VLPs) have applications in both biotechnology and nanotechnology. The capsids of most plant viruses are simple and robust structures and can be produced in large quantities either by the infection of plants or by expression in a variety of heterologous systems. Plant virus particles can be modified genetically and chemically to encapsulate foreign material and can be incorporated into supramolecular structures for use in biotechnology.[224]

Bacterial viruses

Main article: Bacteriophage
An electron micrograph showing a portion of a bacterium covered with viruses
Transmission electron micrograph of multiple bacteriophages attached to a bacterial cell wall

Bacteriophages are a common and diverse group of viruses and are the most abundant biological entity in aquatic environments—there are up to ten times more of these viruses in the oceans than there are bacteria,[225] reaching levels of 250,000,000 bacteriophages per millilitre of seawater.[226] These viruses infect specific bacteria by binding to surface receptor molecules and then entering the cell. Within a short amount of time, in some cases, just minutes, bacterial polymerase starts translating viral mRNA into protein. These proteins go on to become either new virions within the cell, helper proteins, which help assembly of new virions, or proteins involved in cell lysis. Viral enzymes aid in the breakdown of the cell membrane, and, in the case of the T4 phage, in just over twenty minutes after injection over three hundred phages could be released.[227]

The major way bacteria defend themselves from bacteriophages is by producing enzymes that destroy foreign DNA. These enzymes, called restriction endonucleases, cut up the viral DNA that bacteriophages inject into bacterial cells.[228] Bacteria also contain a system that uses CRISPR sequences to retain fragments of the genomes of viruses that the bacteria have come into contact with in the past, which allows them to block the virus's replication through a form of RNA interference.[229][230] This genetic system provides bacteria with acquired immunity to infection.[231]

Some bacteriophages are called "temperate" because they cause latent infections and do not immediately destroy their host cells. Instead, their DNA is incorporated with the host cell's as a prophage. These latent infections become productive when the prophage DNA is activated by stimuli such as changes in the environment.[232] The intestines of animals, including humans, contain temperate bacteriophages, which are activated by various stimuli including changes in diet and antibiotics.[233] Although first observed in bacteriophages, many other viruses are known to form proviruses including HIV.[232][234]

Archaeal viruses

Main article: Archaeal virus

Some viruses replicate within archaea: these are DNA viruses with unusual and sometimes unique shapes.[4][68] These viruses have been studied in most detail in the thermophilic archaea, particularly the orders Sulfolobales and Thermoproteales.[235] Defences against these viruses involve RNA interference from repetitive DNA sequences within archaean genomes that are related to the genes of the viruses.[236][237] Most archaea have CRISPR–Cas systems as an adaptive defence against viruses. These enable archaea to retain sections of viral DNA, which are then used to target and eliminate subsequent infections by the virus using a process similar to RNA interference.[238]

Role in aquatic ecosystems

Main article: Marine virus

Viruses are the most abundant biological entity in aquatic environments.[2] There are about ten million of them in a teaspoon of seawater.[239] Most of these viruses are bacteriophages infecting heterotrophic bacteria and cyanophages infecting cyanobacteria and they are essential to the regulation of saltwater and freshwater ecosystems.[240] Bacteriophages are harmless to plants and animals, and are essential to the regulation of marine and freshwater ecosystems[241] are important mortality agents of phytoplankton, the base of the foodchain in aquatic environments.[242] They infect and destroy bacteria in aquatic microbial communities, and are one of the most important mechanisms of recycling carbon and nutrient cycling in marine environments. The organic molecules released from the dead bacterial cells stimulate fresh bacterial and algal growth, in a process known as the viral shunt.[243] In particular, lysis of bacteria by viruses has been shown to enhance nitrogen cycling and stimulate phytoplankton growth.[244] Viral activity may also affect the biological pump, the process whereby carbon is sequestered in the deep ocean.[245]

Microorganisms constitute more than 90% of the biomass in the sea. It is estimated that viruses kill approximately 20% of this biomass each day and that there are 10 to 15 times as many viruses in the oceans as there are bacteria and archaea.[246] Viruses are also major agents responsible for the destruction of phytoplankton including harmful algal blooms,[247] The number of viruses in the oceans decreases further offshore and deeper into the water, where there are fewer host organisms.[245]

In January 2018, scientists reported that 800 million viruses, mainly of marine origin, are deposited daily from the Earth's atmosphere onto every square meter of the planet's surface, as the result of a global atmospheric stream of viruses, circulating above the weather system but below the altitude of usual airline travel, distributing viruses around the planet.[248][249]

Like any organism, marine mammals are susceptible to viral infections. In 1988 and 2002, thousands of harbour seals were killed in Europe by phocine distemper virus.[250] Many other viruses, including caliciviruses, herpesviruses, adenoviruses and parvoviruses, circulate in marine mammal populations.[245]

In December 2022, scientists reported the first observation of virovory via an experiment on pond water containing chlorovirus, which commonly infects green algae in freshwater environments. When all other microbial food sources were removed from the water, the ciliate Halteria was observed to have increased in number due to the active consumption of chlorovirus as a food source instead of its typical bacterivore diet.[251][252]

Role in evolution

Main article: Horizontal gene transfer

Viruses are an important natural means of transferring genes between different species, which increases genetic diversity and drives evolution.[9][253] It is thought that viruses played a central role in early evolution, before the diversification of the last universal common ancestor into bacteria, archaea and eukaryotes.[254] Viruses are still one of the largest reservoirs of unexplored genetic diversity on Earth.[245]

Applications

Life sciences and medicine

Scientist studying the H5N1 influenza virus

Viruses are important to the study of molecular and cell biology as they provide simple systems that can be used to manipulate and investigate the functions of cells.[255] The study and use of viruses have provided valuable information about aspects of cell biology.[256] For example, viruses have been useful in the study of genetics and helped our understanding of the basic mechanisms of molecular genetics, such as DNA replication, transcription, RNA processing, translation, protein transport, and immunology.

Geneticists often use viruses as vectors to introduce genes into cells that they are studying. This is useful for making the cell produce a foreign substance, or to study the effect of introducing a new gene into the genome. Similarly, virotherapy uses viruses as vectors to treat various diseases, as they can specifically target cells and DNA. It shows promising use in the treatment of cancer and in gene therapy. Eastern European scientists have used phage therapy as an alternative to antibiotics for some time, and interest in this approach is increasing, because of the high level of antibiotic resistance now found in some pathogenic bacteria.[257] The expression of heterologous proteins by viruses is the basis of several manufacturing processes that are currently being used for the production of various proteins such as vaccine antigens and antibodies. Industrial processes have been recently developed using viral vectors and several pharmaceutical proteins are currently in pre-clinical and clinical trials.[258]

Virotherapy

Main article: Virotherapy

Virotherapy involves the use of genetically modified viruses to treat diseases.[259] Viruses have been modified by scientists to reproduce in cancer cells and destroy them but not infect healthy cells. Talimogene laherparepvec (T-VEC), for example, is a modified herpes simplex virus that has had a gene, which is required for viruses to replicate in healthy cells, deleted and replaced with a human gene (GM-CSF) that stimulates immunity. When this virus infects cancer cells, it destroys them and in doing so the presence the GM-CSF gene attracts dendritic cells from the surrounding tissues of the body. The dendritic cells process the dead cancer cells and present components of them to other cells of the immune system.[260] Having completed successful clinical trials, the virus gained approval for the treatment of melanoma in late 2015.[261] Viruses that have been reprogrammed to kill cancer cells are called oncolytic viruses.[262]

Materials science and nanotechnology

From the viewpoint of a materials scientist, viruses can be regarded as organic nanoparticles.[263] Their surface carries specific tools that enable them to cross the barriers of their host cells. The size and shape of viruses and the number and nature of the functional groups on their surface are precisely defined. As such, viruses are commonly used in materials science as scaffolds for covalently linked surface modifications. A particular quality of viruses is that they can be tailored by directed evolution. The powerful techniques developed by life sciences are becoming the basis of engineering approaches towards nanomaterials, opening a wide range of applications far beyond biology and medicine.[264] Because of their size, shape, and well-defined chemical structures, viruses have been used as templates for organising materials on the nanoscale. Examples include the work at the Naval Research Laboratory in Washington, D.C., using Cowpea mosaic virus (CPMV) particles to amplify signals in DNA microarray based sensors. In this application, the virus particles separate the fluorescent dyes used for signalling to prevent the formation of non-fluorescent dimers that act as quenchers.[265] Another example is the use of CPMV as a nanoscale breadboard for molecular electronics.[266]

Synthetic viruses

Many viruses can be synthesised de novo ("from scratch"). The first synthetic virus was created in 2002.[267] Although somewhat of a misconception, it is not the actual virus that is synthesised, but rather its DNA genome (in case of a DNA virus), or a cDNA copy of its genome (in case of RNA viruses). For many virus families the naked synthetic DNA or RNA (once enzymatically converted back from the synthetic cDNA) is infectious when introduced into a cell. That is, they contain all the necessary information to produce new viruses. This technology is now being used to investigate novel vaccine strategies.[268] The ability to synthesise viruses has far-reaching consequences, since viruses can no longer be regarded as extinct, as long as the information of their genome sequence is known and permissive cells are available. As of June 2021, the full-length genome sequences of 11,464 different viruses, including smallpox, are publicly available in an online database maintained by the National Institutes of Health.[269]

Weapons

Further information: Biological warfare

The ability of viruses to cause devastating epidemics in human societies has led to the concern that viruses could be weaponised for biological warfare. Further concern was raised by the successful recreation of the infamous 1918 influenza virus in a laboratory.[270] The smallpox virus devastated numerous societies throughout history before its eradication. There are only two centres in the world authorised by the WHO to keep stocks of smallpox virus: the State Research Center of Virology and Biotechnology VECTOR in Russia and the Centers for Disease Control and Prevention in the United States.[271] It may be used as a weapon,[271] as the vaccine for smallpox sometimes had severe side-effects, it is no longer used routinely in any country. Thus, much of the modern human population has almost no established resistance to smallpox and would be vulnerable to the virus.[271]

See also

  • Cross-species transmission
  • Glossary of virology
  • Law of declining virulence – Disproved hypothesis of epidemiologist Theobald Smith
  • Non-cellular life
  • Retrozyme
  • Smallest organisms
  • Theory of virulence – Theory by biologist Paul W. Ewald
  • Viral metagenomics
  • Viroplasm
  • Zoonosis

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Bibliography

  • Collier L, Balows A, Sussman M (1998). Mahy B, Collier LA (eds.). Topley and Wilson's Microbiology and Microbial Infections. Virology. Vol. 1 (9th ed.). ISBN 0-340-66316-2.
  • Dimmock NJ, Easton AJ, Leppard K (2007). Introduction to Modern Virology (6th ed.). Blackwell Publishing. ISBN 978-1-4051-3645-7.
  • Knipe DM, Howley PM, Griffin DE, Lamb RA, Martin MA, Roizman B, Straus SE (2007). Fields Virology. Lippincott Williams & Wilkins. ISBN 978-0-7817-6060-7.
  • Krasner, Robert (2014). The microbial challenge: a public health perspective. Burlington, Mass: Jones & Bartlett Learning. ISBN 978-1-4496-7375-8. OCLC 794228026.
  • Shors T (2017). Understanding Viruses. Jones and Bartlett Publishers. ISBN 978-1-284-02592-7.

External links

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Microbiology: Virus
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Taxon identifiers
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  • BOLD: 782766
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